Author: Andreas Tille <tille@debian.org>
Last-Update: 2017-09-22
Description: Fix spelling issues
Forwarded: not-needed

--- a/src/dynlibsrc/hscore.c
+++ b/src/dynlibsrc/hscore.c
@@ -413,7 +413,7 @@
   if( hs->st_len == 0 ) {
     new = new_DataScoreStorage();
     if( new == NULL ) {
-      warn("could not make inital data score storage!");
+      warn("could not make initial data score storage!");
       return NULL;
     }
     add_st_Hscore(hs,new);
--- a/src/dynlibsrc/hscore.dy
+++ b/src/dynlibsrc/hscore.dy
@@ -422,7 +422,7 @@
   if( hs->st_len == 0 ) {
     new = new_DataScoreStorage();
     if( new == NULL ) {
-      warn("could not make inital data score storage!");
+      warn("could not make initial data score storage!");
       return NULL;
     }
     add_st_Hscore(hs,new);
--- a/docs/dynamite.tex
+++ b/docs/dynamite.tex
@@ -240,7 +240,7 @@
 communication is on a biologically 'logical' level so theoretically
 one can drop out the dynamite run-time library, replace it with one's
 own specific biological typed library (the ncbi toolkit for example)
-and recompile with a new 'methods' file. This has to assumme that
+and recompile with a new 'methods' file. This has to assume that
 certain biological concepts are represented in a particular way (for
 example, Base A is represented by 0, Base C 1 etc), but does allow the
 underlying data structures complete freedom.
@@ -2839,7 +2839,7 @@
 Once all the semantics of the Dynamite blueprint is ok, the compiler then turns its
 attention to the calc lines. This is like a mini-parser operating inside the dynamite
 parser, but unlike the dynamite parser, this once was written in yacc/lex and is
-a more vanilla parser enviroment.
+a more vanilla parser environment.
 
 \subsubsection{Parser Syntax error on calc line}
 
--- a/docs/wise2.tex
+++ b/docs/wise2.tex
@@ -121,7 +121,7 @@
         Could not read a GeneFrequency file in human.gf
 ...
 \end{verbatim}
-This means that the enviroment variable WISECONFIGDIR has not been
+This means that the environment variable WISECONFIGDIR has not been
 set up correctly. You need to find where the distribution was downloaded
 to (a directory called something like wise2.1.16b) and inside that
 directory should be the configuration directory wisecfg. You need to
@@ -427,14 +427,14 @@
 \begin{verbatim}
 genewisedb -pfam Pfam -dnas myseq.fa
 \end{verbatim}
-If you have set up the HMMER package to work with Pfam using the enviroment
+If you have set up the HMMER package to work with Pfam using the environment
 variable HMMERDB, Wise2 will also pick that up as well.
 
 
 
 \subsubsection{Optimising alignment speed}
 
-Wise2 assummes you have a rather small amount of memory (20 MBytes).
+Wise2 assumes you have a rather small amount of memory (20 MBytes).
 When it is making an alignment, if it cannot make the explicit matrix
 in that size (being length of query $\times$ length of target $\times$
 state number) it has to move to linear memory (length of query
@@ -444,7 +444,7 @@
 If you have more memory than 20 Mbytes, then it is really sensible to
 up the number, using the -kbyte option. For a machine with say
 64Mbytes physical memory I would suggest putting an upper limit of
-50Mbytes with -kbyte. This does assumme you are not using it for
+50Mbytes with -kbyte. This does assume you are not using it for
 anything else.
 
 You can change the compile time default in basematrix.h if you can't
@@ -576,7 +576,7 @@
 (of course, your version of Wise2 might be different). 
 
 Once you have made the tar file, it should build completely cleanly as
-long as you have an ANSI C compiler. If in doubt, just assumme that it
+long as you have an ANSI C compiler. If in doubt, just assume that it
 is, but in particular sun users might want to use gcc (gnu cc) as the
 sun cc compiler installed by default is often non-ANSI. To change the
 cc compiler you only need to edit the line in the top level makefile
@@ -675,7 +675,7 @@
 of the probability.
 
 Perhaps a better known example is the relationship between the old
-profile technology, as developped by Gribskov and Gibson along with
+profile technology, as developed by Gribskov and Gibson along with
 others, and its probabilistic partner, profile Hidden Markov Models
 (profile HMMs).  In terms of the actual algorithm these two methods
 are very similar: it is simply that the profile HMM has a strong
@@ -804,7 +804,7 @@
 given in half bits, in other words using a 2*log2 mapping from
 probability space to the give scores in the matrix.  By reversing this
 process one can get pretty good emission probability for the amino
-acids. I now assumme that the gap penalities are \emph{as if} they were
+acids. I now assume that the gap penalities are \emph{as if} they were
 written in half bits. A certain amount of normalisation is required to
 make sure things add to one, and eh voila - one profile HMM from a
 single sequence.
@@ -870,7 +870,7 @@
 splice sites overlap between their consensi and the coding sequence
 region. These overlaps need to be treated correctly: the problem is
 that probabilistically we have two processes wanting to account for
-the same DNA bases. This was solved by assumming conditional
+the same DNA bases. This was solved by assuming conditional
 independence between the two processes. A more formal mathematicall
 approach can be found in the documented called 'probappendix'.
 
@@ -1075,7 +1075,7 @@
 searches.
 
 I have been thinking about using a classical statistic method on top
-of the bit score, assumming the distribution is an extreme value
+of the bit score, assuming the distribution is an extreme value
 distribution (EVD), but for DNA it becomes difficult to know what to
 do with the problem of different lengths of DNA. As these can be
 wildly different, it is hard to know precisely how to handle
@@ -1222,12 +1222,12 @@
 \item[-gene] [human.gf] Gene parameter file. Provide statistics for
 different gene models. Current human.gf and worm.gf are provided. The
 statistics are basically too complicated to explain here.
-\item[-subs] [1e-05] Substitution error rate, ie the assummed
+\item[-subs] [1e-05] Substitution error rate, ie the assumed
 probability of base substitutions in the sequencing reaction/assembly
 that provided the DNA sequence. The substituion error is what
 dominates the penalty for stop codons - a higher error rate implies a
 smaller penalty for stop codons
-\item[-indel] [1e-05] Insertion/deletion error rate, ie the assummed
+\item[-indel] [1e-05] Insertion/deletion error rate, ie the assumed
 probability of indel events in the sequencing reaction/assembly that
 provided the DNA sequence. The indel rate is what provides the penalty
 for frameshift errors. A higher error rate implies a smaller penalty
@@ -1475,10 +1475,10 @@
 
 \item[-codon]  [codon.table]  Codon file. The default is for the universal code, but
 you can supply your own
-\item[-subs]   [0.01] Substitution error rate, ie the assummed probability of base substitutions
+\item[-subs]   [0.01] Substitution error rate, ie the assumed probability of base substitutions
 in the sequencing reaction/assembly that provided the DNA sequence. The substituion error is what dominates
 the penalty for stop codons - a higher error rate implies a smaller penalty for stop codons
-\item[-indel]  [0.01] Insertion/deletion error rate, ie the assummed probability of indel events
+\item[-indel]  [0.01] Insertion/deletion error rate, ie the assumed probability of indel events
 in the sequencing reaction/assembly that provided the DNA sequence. The indel rate is what provides
 the penalty for frameshift errors. A higher error rate implies a smaller penalty for indels.
 \item[-null]   [syn/flat]   Random Model as synchronous or flat [default syn]
@@ -1580,8 +1580,8 @@
 for that matter, but in theory it should work better for orthologous
 regulatory regions, depending on how much active change you expect
 paralogous regulatory regions to have). Promoterwise reports alignments 
-between these two sequences assumming that alignments cannot overlap in
-both sequences, but *not* assumming that the alignments have to be co
+between these two sequences assuming that alignments cannot overlap in
+both sequences, but *not* assuming that the alignments have to be co
 linear or on the same strand.
 
 
@@ -1639,7 +1639,7 @@
 \subsection{dba - Dna Block Aligner}
 \label{sec:dba}
 
-dba - standing for Dna Block Aligner, was developped by Niclas Jareborg,
+dba - standing for Dna Block Aligner, was developed by Niclas Jareborg,
 Richard Durbin and Ewan Birney for characterising shared regulatory regions
 of genomic DNA, either in upstream regions or introns of genes
 
--- a/src/base/wisefile.c
+++ b/src/base/wisefile.c
@@ -295,7 +295,7 @@
     return ifp;
   
   else if ( shouldreporterror )
-    log_full_error(INFO,0,"Expanded personal direcotry open for[%s,%s], expanded to %s failed: Error message is %s",filename,prot,buffer,ERRORSTR);
+    log_full_error(INFO,0,"Expanded personal directory open for[%s,%s], expanded to %s failed: Error message is %s",filename,prot,buffer,ERRORSTR);
   
   
   /* next line ABSOLUTELY relies on order of evaluation */
@@ -329,7 +329,7 @@
  *
  *
  *
- * Arg:         envname [READ ] enviroment variable to read from [NullString]
+ * Arg:         envname [READ ] environment variable to read from [NullString]
  * Arg:        filename [UNKN ] Undocumented argument [char *]
  * Arg:            name [READ ] filename to open [NullString]
  * Arg:             env [UNKN ] Undocumented argument [char *]
@@ -344,17 +344,17 @@
   char path [512];
 
   if( filename == NULL || env == NULL ) {
-    warn("Passed a NULL filename or enviroment name into Envfile. Should trap this elsewhere");
+    warn("Passed a NULL filename or environment name into Envfile. Should trap this elsewhere");
     return NULL;
   }
 
   if( (envp = getenv(env)) == NULL ) {
-    /* fail gracefully - somebody might query a number of enviroment variables */
+    /* fail gracefully - somebody might query a number of environment variables */
     return NULL;
   }
 
   if( strlen(filename) + strlen(envp) < 490 ) {
-    warn("Really long filename/enviroment variables [%s] [%s] Can't cope!",filename,envp);
+    warn("Really long filename/environment variables [%s] [%s] Can't cope!",filename,envp);
     return NULL;
   }
   sprintf(path,"%s/%s",filename,envp);
--- a/src/base/wisefile.dy
+++ b/src/base/wisefile.dy
@@ -269,7 +269,7 @@
     return ifp;
   
   else if ( shouldreporterror )
-    log_full_error(INFO,0,"Expanded personal direcotry open for[%s,%s], expanded to %s failed: Error message is %s",filename,prot,buffer,ERRORSTR);
+    log_full_error(INFO,0,"Expanded personal directory open for[%s,%s], expanded to %s failed: Error message is %s",filename,prot,buffer,ERRORSTR);
   
   
   /* next line ABSOLUTELY relies on order of evaluation */
@@ -302,7 +302,7 @@
 
 %arg
 name r filename to open
-envname r enviroment variable to read from
+envname r environment variable to read from
 return a valid file pointer or NULL
 %%
 FILE * envopenfile(char * filename,char * env)
@@ -311,17 +311,17 @@
   char path [512];
 
   if( filename == NULL || env == NULL ) {
-    warn("Passed a NULL filename or enviroment name into Envfile. Should trap this elsewhere");
+    warn("Passed a NULL filename or environment name into Envfile. Should trap this elsewhere");
     return NULL;
   }
 
   if( (envp = getenv(env)) == NULL ) {
-    /* fail gracefully - somebody might query a number of enviroment variables */
+    /* fail gracefully - somebody might query a number of environment variables */
     return NULL;
   }
 
   if( strlen(filename) + strlen(envp) < 490 ) {
-    warn("Really long filename/enviroment variables [%s] [%s] Can't cope!",filename,envp);
+    warn("Really long filename/environment variables [%s] [%s] Can't cope!",filename,envp);
     return NULL;
   }
   sprintf(path,"%s/%s",filename,envp);
--- a/src/base/wisefile.h
+++ b/src/base/wisefile.h
@@ -143,7 +143,7 @@
  *
  *
  *
- * Arg:         envname [READ ] enviroment variable to read from [NullString]
+ * Arg:         envname [READ ] environment variable to read from [NullString]
  * Arg:        filename [UNKN ] Undocumented argument [char *]
  * Arg:            name [READ ] filename to open [NullString]
  * Arg:             env [UNKN ] Undocumented argument [char *]
--- a/LICENSE
+++ b/LICENSE
@@ -19,7 +19,7 @@
 
 The HMMer2 libaries (Sean Eddy's HMM package) and the models directory
 (The algorithms for the Wise2 package, and final executable programs)
-are both distributed under a Gnu General Public License (GPL). This
+are both distributed under a GNU General Public License (GPL). This
 means that the entire package as it is distributed with these portions
 in is also licensed under GPL, due to the 'infectious' nature of the
 GPL.
--- a/docs/wise3arch.tex
+++ b/docs/wise3arch.tex
@@ -49,7 +49,7 @@
 
 \subsection{Committment to open source, freely available code}
 
-The Wise2 package has been licensed under the Gnu Public License since
+The Wise2 package has been licensed under the GNU General Public License since
 its inception.  In addition, parts of the package has even less
 restrictive Licenses. I have a strong committment to keep Wise a
 freely available, open source package. The aim of the open
--- a/src/corba/scanwise_protein_index.c
+++ b/src/corba/scanwise_protein_index.c
@@ -19,7 +19,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/dnaindex/assembly/badkmer.c
+++ b/src/dnaindex/assembly/badkmer.c
@@ -25,7 +25,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EBI 2003\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/dnaindex/assembly/pathwise.c
+++ b/src/dnaindex/assembly/pathwise.c
@@ -40,7 +40,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EBI 2003\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/dnaindex/bigseqwise.c
+++ b/src/dnaindex/bigseqwise.c
@@ -10,7 +10,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/dnaindex/findbad_kmer.c
+++ b/src/dnaindex/findbad_kmer.c
@@ -13,7 +13,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/dnaindex/kwise.c
+++ b/src/dnaindex/kwise.c
@@ -15,7 +15,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/alignwise.c
+++ b/src/models/alignwise.c
@@ -61,7 +61,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/amplimer_resolver.c
+++ b/src/models/amplimer_resolver.c
@@ -10,7 +10,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/cdnawise.c
+++ b/src/models/cdnawise.c
@@ -15,7 +15,7 @@
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
 
 
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL (2001) and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/clonewise.c
+++ b/src/models/clonewise.c
@@ -25,7 +25,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/dbac.c
+++ b/src/models/dbac.c
@@ -363,7 +363,7 @@
   fprintf(ofp,"  Released %s\n",RELEASE_DAY);  
   fprintf(ofp,"  Compiled %s\n",COMPILE_DATE);  
   fprintf(ofp,"dba was written by Niclas Jareborg, Ewan Birney and Richard Durbin\n");  
-  fprintf(ofp,"Copyright (c) 1998,1999,2000,2001 GRL ltd. It is distributed under a Gnu Public License\n");  
+  fprintf(ofp,"Copyright (c) 1998,1999,2000,2001 GRL ltd. It is distributed under a GNU General Public License\n");  
   fprintf(ofp,"See GNULICENSE in source directory for more information\n");  
 }  
 
--- a/src/models/dnal.c
+++ b/src/models/dnal.c
@@ -104,7 +104,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/dnawise.c
+++ b/src/models/dnawise.c
@@ -8,7 +8,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/editdist.c
+++ b/src/models/editdist.c
@@ -8,7 +8,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/estwise.c
+++ b/src/models/estwise.c
@@ -557,7 +557,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/estwisedb.c
+++ b/src/models/estwisedb.c
@@ -206,7 +206,7 @@
 
   if( make_anchored_aln == TRUE ) {
     if( tsm == NULL ) {
-      warn("Attempting to make an achored alignment without a HMM. impossible!");
+      warn("Attempting to make an anchored alignment without a HMM. impossible!");
       make_anchored_aln = FALSE;
     } else {
       anchored = single_unit_AlnBlock(tsm->len,"MATCH_STATE");
@@ -807,7 +807,7 @@
   fprintf(ofp,"-------------------------------------------------------------\n");
   fprintf(ofp,"Wise2 - database searching mode\n");
   fprintf(ofp,"Program: %s version: %s released: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY);
-  fprintf(ofp,"This program is freely distributed under a Gnu Public License.\n");
+  fprintf(ofp,"This program is freely distributed under a GNU General Public License.\n");
   fprintf(ofp,"   See -version for more info on copyright\n");
   fprintf(ofp,"Bugs and credits to Ewan Birney <birney@sanger.ac.uk>\n");
   fprintf(ofp,"-------------------------------------------------------------\n\n");
@@ -836,7 +836,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/evopairwise.c
+++ b/src/models/evopairwise.c
@@ -15,7 +15,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/fivestar.c
+++ b/src/models/fivestar.c
@@ -14,7 +14,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/fivestarscan.c
+++ b/src/models/fivestarscan.c
@@ -14,7 +14,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/fivestarsearch.c
+++ b/src/models/fivestarsearch.c
@@ -12,7 +12,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/genewise.c
+++ b/src/models/genewise.c
@@ -858,7 +858,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/genewisedb.c
+++ b/src/models/genewisedb.c
@@ -505,7 +505,7 @@
 {
   fprintf(ofp,"Wise2 - database searching mode\n");
   fprintf(ofp,"Program: %s version: %s released: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY);
-  fprintf(ofp,"This program is freely distributed under a Gnu Public License.\n");
+  fprintf(ofp,"This program is freely distributed under a GNU General Public License.\n");
   fprintf(ofp,"   See -version for more info on copyright\n");
   fprintf(ofp,"Bugs and credits to Ewan Birney <birney@sanger.ac.uk>\n");
   fprintf(ofp,"-----------------------------------------------------\n\n");
@@ -1003,7 +1003,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/genomewise.c
+++ b/src/models/genomewise.c
@@ -16,7 +16,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/lba.c
+++ b/src/models/lba.c
@@ -8,7 +8,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/motifcluster.c
+++ b/src/models/motifcluster.c
@@ -8,7 +8,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/motifdiff.c
+++ b/src/models/motifdiff.c
@@ -8,7 +8,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/motifwise.c
+++ b/src/models/motifwise.c
@@ -8,7 +8,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/oldpostwise.c
+++ b/src/models/oldpostwise.c
@@ -375,7 +375,7 @@
 void show_version(void)
 {
   fprintf(stdout,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(stdout,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(stdout,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(stdout,"The source code is copyright (c) GRL 1998 and others\n");
   fprintf(stdout,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(stdout,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/promotercluster.c
+++ b/src/models/promotercluster.c
@@ -7,7 +7,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/promoterwise.c
+++ b/src/models/promoterwise.c
@@ -15,7 +15,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/pseudowise.c
+++ b/src/models/pseudowise.c
@@ -13,7 +13,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/psw.c
+++ b/src/models/psw.c
@@ -259,7 +259,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/pswdb.c
+++ b/src/models/pswdb.c
@@ -95,7 +95,7 @@
 void show_version(void)
 {
   fprintf(stdout,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(stdout,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(stdout,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(stdout,"The source code is copyright (c) EMBL 1998 and others\n");
   fprintf(stdout,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(stdout,"For more information read the GNULICENSE file in the distribution\n\n");
@@ -347,7 +347,7 @@
   fprintf(ofp,"-------------------------------------------------------------\n");
   fprintf(ofp,"Wise2 - Protein vs. Protein\n");
   fprintf(ofp,"Program: %s version: %s released: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY);
-  fprintf(ofp,"This program is freely distributed under a Gnu Public License.\n");
+  fprintf(ofp,"This program is freely distributed under a GNU General Public License.\n");
   fprintf(ofp,"   See -version for more info on copyright\n");
   fprintf(ofp,"Bugs and credits to: Richard Copley <copley@embl-heidelberg.de>\n"); 
   fprintf(ofp,"                     Ewan Birney <birney@sanger.ac.uk>\n");
--- a/src/models/scanwisep.c
+++ b/src/models/scanwisep.c
@@ -421,7 +421,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/statwise.c
+++ b/src/models/statwise.c
@@ -11,7 +11,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/sywise.c
+++ b/src/models/sywise.c
@@ -12,7 +12,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/network/wise_proteinindex_server.c
+++ b/src/network/wise_proteinindex_server.c
@@ -26,7 +26,7 @@
 void show_version(FILE * ofp)
 {
   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
+  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/test/estwise-db.out
+++ b/src/test/estwise-db.out
@@ -1,7 +1,7 @@
 -------------------------------------------------------------
 Wise2 - database searching mode
 Program: estwisedb version: $Name: wise2-4-1 $ released: unreleased
-This program is freely distributed under a Gnu Public License.
+This program is freely distributed under a GNU General Public License.
    See -version for more info on copyright
 Bugs and credits to Ewan Birney <birney@sanger.ac.uk>
 -------------------------------------------------------------
--- a/src/test/genewise-db-lite.out
+++ b/src/test/genewise-db-lite.out
@@ -1,6 +1,6 @@
 Wise2 - database searching mode
 Program: genewisedb version: $Name: wise2-4-1 $ released: unreleased
-This program is freely distributed under a Gnu Public License.
+This program is freely distributed under a GNU General Public License.
    See -version for more info on copyright
 Bugs and credits to Ewan Birney <birney@sanger.ac.uk>
 -----------------------------------------------------
--- a/src/test/genewise-db.out
+++ b/src/test/genewise-db.out
@@ -1,6 +1,6 @@
 Wise2 - database searching mode
 Program: genewisedb version: $Name: wise2-4-1 $ released: unreleased
-This program is freely distributed under a Gnu Public License.
+This program is freely distributed under a GNU General Public License.
    See -version for more info on copyright
 Bugs and credits to Ewan Birney <birney@sanger.ac.uk>
 -----------------------------------------------------
--- a/src/test/genewisedb-pfam.out
+++ b/src/test/genewisedb-pfam.out
@@ -1,6 +1,6 @@
 Wise2 - database searching mode
 Program: genewisedb version: $Name: wise2-4-1 $ released: unreleased
-This program is freely distributed under a Gnu Public License.
+This program is freely distributed under a GNU General Public License.
    See -version for more info on copyright
 Bugs and credits to Ewan Birney <birney@sanger.ac.uk>
 -----------------------------------------------------
--- a/src/test/pswdb.out
+++ b/src/test/pswdb.out
@@ -1,7 +1,7 @@
 -------------------------------------------------------------
 Wise2 - Protein vs. Protein
 Program: pswdb version: $Name: wise2-4-1 $ released: unreleased
-This program is freely distributed under a Gnu Public License.
+This program is freely distributed under a GNU General Public License.
    See -version for more info on copyright
 Bugs and credits to: Richard Copley <copley@embl-heidelberg.de>
                      Ewan Birney <birney@sanger.ac.uk>
--- a/src/models/genefrequency.c
+++ b/src/models/genefrequency.c
@@ -459,7 +459,7 @@
 
     if( strwhitestartcmp(buffer,"type",spacestr) == 0 ) {
 
-      phase = 3; /** if no phase, assumme it is for all phases **/
+      phase = 3; /** if no phase, assume it is for all phases **/
 
       type = check_type_GeneFrequency(buffer,ifp,&center,&phase);
       
@@ -636,7 +636,7 @@
   ret = strtod(runner,&end);
 
   if( end == runner || isalnum((int)*end) ) {
-    warn("Bad conversion of string [%s] to double [%f] occured",runner,ret);
+    warn("Bad conversion of string [%s] to double [%f] occurred",runner,ret);
   }
 
   return ret;
@@ -810,7 +810,7 @@
   
 /* Function:  read_base_GeneConsensus(base_array,line,ifp)
  *
- * Descrip:    assummes base_array is 4 positions long
+ * Descrip:    assumes base_array is 4 positions long
  *               
  *             line should have begin consensus on it and be of MAXLINE length as it will be used as the buffer.
  *               
@@ -877,7 +877,7 @@
 
 /* Function:  read_codon_GeneConsensus(codon_array,line,ifp)
  *
- * Descrip:    assummes codon_array is 64 positions long
+ * Descrip:    assumes codon_array is 64 positions long
  *               
  *             line should have begin consensus on it and be of MAXLINE length as it will be used as the buffer.
  *
--- a/src/models/genefrequency.dy
+++ b/src/models/genefrequency.dy
@@ -428,7 +428,7 @@
 
     if( strwhitestartcmp(buffer,"type",spacestr) == 0 ) {
 
-      phase = 3; /** if no phase, assumme it is for all phases **/
+      phase = 3; /** if no phase, assume it is for all phases **/
 
       type = check_type_GeneFrequency(buffer,ifp,&center,&phase);
       
@@ -597,7 +597,7 @@
   ret = strtod(runner,&end);
 
   if( end == runner || isalnum((int)*end) ) {
-    warn("Bad conversion of string [%s] to double [%f] occured",runner,ret);
+    warn("Bad conversion of string [%s] to double [%f] occurred",runner,ret);
   }
 
   return ret;
@@ -745,7 +745,7 @@
 }
   
 %func
-assummes base_array is 4 positions long
+assumes base_array is 4 positions long
   
 line should have begin consensus on it and be of MAXLINE length as it will be used as the buffer.
   
@@ -802,7 +802,7 @@
 
 
 %func
-assummes codon_array is 64 positions long
+assumes codon_array is 64 positions long
   
 line should have begin consensus on it and be of MAXLINE length as it will be used as the buffer.
 
--- a/src/models/seqerror.dy
+++ b/src/models/seqerror.dy
@@ -42,7 +42,7 @@
 SequenceErrorSet * ses
 %info
 This holds a sequence and what
-errors have occured in it.
+errors have occurred in it.
 %%
 
 
--- a/src/models/seqerror.h
+++ b/src/models/seqerror.h
@@ -72,7 +72,7 @@
 /* Object ErrorSequence
  *
  * Descrip: This holds a sequence and what
- *        errors have occured in it.
+ *        errors have occurred in it.
  *
  *
  */
--- a/src/dynlibsrc/hspscaninterface.c
+++ b/src/dynlibsrc/hspscaninterface.c
@@ -158,7 +158,7 @@
 void show_help_HSPScanInterfacePara(FILE * ofp)
 {
   fprintf(ofp,"Parameters for word scan\n");
-  fprintf(ofp,"   -hspscan_impl [vanilla/threaded/twohit] implementation to use if compliled for runtime\n");
+  fprintf(ofp,"   -hspscan_impl [vanilla/threaded/twohit] implementation to use if compiled for runtime\n");
   fprintf(ofp,"   -hspscan_maxres    [100] maximum results returned by scan\n");
   fprintf(ofp,"   -hspscan_numb     [1000] word count to numb word (for low complexity)\n");
   fprintf(ofp,"   -hspscan_worddepth   [2] maximum offset from word - [0,1,2]\n");
--- a/src/dynlibsrc/hspscaninterface.dy
+++ b/src/dynlibsrc/hspscaninterface.dy
@@ -157,7 +157,7 @@
 void show_help_HSPScanInterfacePara(FILE * ofp)
 {
   fprintf(ofp,"Parameters for word scan\n");
-  fprintf(ofp,"   -hspscan_impl [vanilla/threaded/twohit] implementation to use if compliled for runtime\n");
+  fprintf(ofp,"   -hspscan_impl [vanilla/threaded/twohit] implementation to use if compiled for runtime\n");
   fprintf(ofp,"   -hspscan_maxres    [100] maximum results returned by scan\n");
   fprintf(ofp,"   -hspscan_numb     [1000] word count to numb word (for low complexity)\n");
   fprintf(ofp,"   -hspscan_worddepth   [2] maximum offset from word - [0,1,2]\n");
--- a/src/dyc/dbthread.c
+++ b/src/dyc/dbthread.c
@@ -311,7 +311,7 @@
       expr(dfp,"holder->%s = %s(holder->querydb,&db_status);",gm->query->name,gm->qtype->init_func);
       expr(dfp,"holder->query_init = TRUE;");
       expr(dfp,"if( db_status == DB_RETURN_ERROR )");
-      hang_expr(dfp,"fatal(\"Unable to initalise query database in %s search\");",gm->name);
+      hang_expr(dfp,"fatal(\"Unable to initialise query database in %s search\");",gm->name);
       closebrace(dfp);
       expr(dfp,"%s = %s(holder->%s);",gm->query->name,gm->qtype->hard_link_func,gm->query->name);
       add_block_comment(dfp,"get query information into datascore");
--- a/src/dyc/dbthread.dy
+++ b/src/dyc/dbthread.dy
@@ -300,7 +300,7 @@
       expr(dfp,"holder->%s = %s(holder->querydb,&db_status);",gm->query->name,gm->qtype->init_func);
       expr(dfp,"holder->query_init = TRUE;");
       expr(dfp,"if( db_status == DB_RETURN_ERROR )");
-      hang_expr(dfp,"fatal(\"Unable to initalise query database in %s search\");",gm->name);
+      hang_expr(dfp,"fatal(\"Unable to initialise query database in %s search\");",gm->name);
       closebrace(dfp);
       expr(dfp,"%s = %s(holder->%s);",gm->query->name,gm->qtype->hard_link_func,gm->query->name);
       add_block_comment(dfp,"get query information into datascore");
--- a/src/models/abc.c
+++ b/src/models/abc.c
@@ -442,7 +442,7 @@
         holder->query = init_ProteinDB(holder->querydb,&db_status);  
         holder->query_init = TRUE;   
         if( db_status == DB_RETURN_ERROR )   
-          fatal("Unable to initalise query database in abc search"); 
+          fatal("Unable to initialise query database in abc search"); 
         }  
       query = hard_link_ComplexSequence(holder->query);  
       /* get query information into datascore */ 
@@ -989,7 +989,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/cdnawise10.c
+++ b/src/models/cdnawise10.c
@@ -694,7 +694,7 @@
         holder->query = init_cDNADB(holder->querydb,&db_status); 
         holder->query_init = TRUE;   
         if( db_status == DB_RETURN_ERROR )   
-          fatal("Unable to initalise query database in CdnaWise10 search");  
+          fatal("Unable to initialise query database in CdnaWise10 search");  
         }  
       query = hard_link_ComplexSequence(holder->query);  
       /* get query information into datascore */ 
@@ -1477,7 +1477,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/estloop3.c
+++ b/src/models/estloop3.c
@@ -697,7 +697,7 @@
         holder->query = init_GeneWiseDB(holder->querydb,&db_status); 
         holder->query_init = TRUE;   
         if( db_status == DB_RETURN_ERROR )   
-          fatal("Unable to initalise query database in EstLoop3 search");    
+          fatal("Unable to initialise query database in EstLoop3 search");    
         }  
       query = hard_link_GeneWiseScore(holder->query);    
       /* get query information into datascore */ 
@@ -1470,7 +1470,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/estquick3.c
+++ b/src/models/estquick3.c
@@ -467,7 +467,7 @@
         holder->query = init_GeneWiseQuickDB(holder->querydb,&db_status);    
         holder->query_init = TRUE;   
         if( db_status == DB_RETURN_ERROR )   
-          fatal("Unable to initalise query database in EstQuick3 search");   
+          fatal("Unable to initialise query database in EstQuick3 search");   
         }  
       query = hard_link_GeneWiseScoreFlat(holder->query);    
       /* get query information into datascore */ 
@@ -1018,7 +1018,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/estslim3.c
+++ b/src/models/estslim3.c
@@ -505,7 +505,7 @@
         holder->query = init_GeneWiseDB(holder->querydb,&db_status); 
         holder->query_init = TRUE;   
         if( db_status == DB_RETURN_ERROR )   
-          fatal("Unable to initalise query database in EstSlim3 search");    
+          fatal("Unable to initialise query database in EstSlim3 search");    
         }  
       query = hard_link_GeneWiseScore(holder->query);    
       /* get query information into datascore */ 
@@ -1094,7 +1094,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/estslimloop.c
+++ b/src/models/estslimloop.c
@@ -594,7 +594,7 @@
         holder->query = init_GeneWiseDB(holder->querydb,&db_status); 
         holder->query_init = TRUE;   
         if( db_status == DB_RETURN_ERROR )   
-          fatal("Unable to initalise query database in EstSlimLoop3 search");    
+          fatal("Unable to initialise query database in EstSlimLoop3 search");    
         }  
       query = hard_link_GeneWiseScore(holder->query);    
       /* get query information into datascore */ 
@@ -1272,7 +1272,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/estwise3.c
+++ b/src/models/estwise3.c
@@ -613,7 +613,7 @@
         holder->query = init_GeneWiseDB(holder->querydb,&db_status); 
         holder->query_init = TRUE;   
         if( db_status == DB_RETURN_ERROR )   
-          fatal("Unable to initalise query database in EstWise3 search");    
+          fatal("Unable to initialise query database in EstWise3 search");    
         }  
       query = hard_link_GeneWiseScore(holder->query);    
       /* get query information into datascore */ 
@@ -1302,7 +1302,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/geneloop21.c
+++ b/src/models/geneloop21.c
@@ -1190,7 +1190,7 @@
         holder->query = init_GeneWiseDB(holder->querydb,&db_status); 
         holder->query_init = TRUE;   
         if( db_status == DB_RETURN_ERROR )   
-          fatal("Unable to initalise query database in GeneLoop21 search");  
+          fatal("Unable to initialise query database in GeneLoop21 search");  
         }  
       query = hard_link_GeneWiseScore(holder->query);    
       /* get query information into datascore */ 
@@ -2444,7 +2444,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/geneloop6.c
+++ b/src/models/geneloop6.c
@@ -682,7 +682,7 @@
         holder->query = init_GeneWiseDB(holder->querydb,&db_status); 
         holder->query_init = TRUE;   
         if( db_status == DB_RETURN_ERROR )   
-          fatal("Unable to initalise query database in GeneLoop6 search");   
+          fatal("Unable to initialise query database in GeneLoop6 search");   
         }  
       query = hard_link_GeneWiseScore(holder->query);    
       /* get query information into datascore */ 
@@ -1426,7 +1426,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/genestretch6.c
+++ b/src/models/genestretch6.c
@@ -717,7 +717,7 @@
         holder->query = init_GeneWiseDB(holder->querydb,&db_status); 
         holder->query_init = TRUE;   
         if( db_status == DB_RETURN_ERROR )   
-          fatal("Unable to initalise query database in GeneStretch6 search");    
+          fatal("Unable to initialise query database in GeneStretch6 search");    
         }  
       query = hard_link_GeneWiseScore(holder->query);    
       /* get query information into datascore */ 
@@ -1500,7 +1500,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/genewise21.c
+++ b/src/models/genewise21.c
@@ -1354,7 +1354,7 @@
         holder->query = init_GeneWiseDB(holder->querydb,&db_status); 
         holder->query_init = TRUE;   
         if( db_status == DB_RETURN_ERROR )   
-          fatal("Unable to initalise query database in GeneWise21 search");  
+          fatal("Unable to initialise query database in GeneWise21 search");  
         }  
       query = hard_link_GeneWiseScore(holder->query);    
       /* get query information into datascore */ 
@@ -2770,7 +2770,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/genewise4.c
+++ b/src/models/genewise4.c
@@ -580,7 +580,7 @@
         holder->query = init_GeneWiseDB(holder->querydb,&db_status); 
         holder->query_init = TRUE;   
         if( db_status == DB_RETURN_ERROR )   
-          fatal("Unable to initalise query database in GeneWise4 search");   
+          fatal("Unable to initialise query database in GeneWise4 search");   
         }  
       query = hard_link_GeneWiseScore(holder->query);    
       /* get query information into datascore */ 
@@ -1226,7 +1226,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/genewise6.c
+++ b/src/models/genewise6.c
@@ -638,7 +638,7 @@
         holder->query = init_GeneWiseDB(holder->querydb,&db_status); 
         holder->query_init = TRUE;   
         if( db_status == DB_RETURN_ERROR )   
-          fatal("Unable to initalise query database in GeneWise6 search");   
+          fatal("Unable to initialise query database in GeneWise6 search");   
         }  
       query = hard_link_GeneWiseScore(holder->query);    
       /* get query information into datascore */ 
@@ -1338,7 +1338,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/gwlite.c
+++ b/src/models/gwlite.c
@@ -597,7 +597,7 @@
         holder->query = init_GwLite_GeneWiseDB(holder->querydb,&db_status);  
         holder->query_init = TRUE;   
         if( db_status == DB_RETURN_ERROR )   
-          fatal("Unable to initalise query database in GeneLiteModel search");   
+          fatal("Unable to initialise query database in GeneLiteModel search");   
         }  
       query = hard_link_GwLiteScore(holder->query);  
       /* get query information into datascore */ 
@@ -1275,7 +1275,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/pba.c
+++ b/src/models/pba.c
@@ -496,7 +496,7 @@
         holder->q = init_ProteinDB(holder->querydb,&db_status);  
         holder->query_init = TRUE;   
         if( db_status == DB_RETURN_ERROR )   
-          fatal("Unable to initalise query database in ProteinBlockAligner search"); 
+          fatal("Unable to initialise query database in ProteinBlockAligner search"); 
         }  
       q = hard_link_ComplexSequence(holder->q);  
       /* get query information into datascore */ 
@@ -1102,7 +1102,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/proteinsw.c
+++ b/src/models/proteinsw.c
@@ -444,7 +444,7 @@
         holder->query = init_ProteinDB(holder->querydb,&db_status);  
         holder->query_init = TRUE;   
         if( db_status == DB_RETURN_ERROR )   
-          fatal("Unable to initalise query database in ProteinSW search");   
+          fatal("Unable to initialise query database in ProteinSW search");   
         }  
       query = hard_link_ComplexSequence(holder->query);  
       /* get query information into datascore */ 
@@ -988,7 +988,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/pseudowise7.c
+++ b/src/models/pseudowise7.c
@@ -649,7 +649,7 @@
         holder->query = init_GeneWiseDB(holder->querydb,&db_status); 
         holder->query_init = TRUE;   
         if( db_status == DB_RETURN_ERROR )   
-          fatal("Unable to initalise query database in PseudoWise7 search"); 
+          fatal("Unable to initialise query database in PseudoWise7 search"); 
         }  
       query = hard_link_GeneWiseScore(holder->query);    
       /* get query information into datascore */ 
@@ -1368,7 +1368,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/sw_wrap.dy
+++ b/src/models/sw_wrap.dy
@@ -311,7 +311,7 @@
 
 %func
 This is the most correct way of aligning two Proteins,
-using Protein objects, which can be assummed to be
+using Protein objects, which can be assumed to be
 proteins with no objections
 
 To display the alignment use write_pretty_Protein_align
@@ -359,7 +359,7 @@
    out = std_score_Hscore(bits_cutoff,report_level);
 
    if( dbsi == NULL ) {
-      warn("Passed a NULL dbsi search implementaion object. Exiting without searching");
+      warn("Passed a NULL dbsi search implementation object. Exiting without searching");
       goto exit;
    }
 
@@ -411,7 +411,7 @@
    out = std_score_Hscore(bits_cutoff,report_level);
 
    if( dbsi == NULL ) {
-      warn("Passed a NULL dbsi search implementaion object. Exiting without searching");
+      warn("Passed a NULL dbsi search implementation object. Exiting without searching");
       goto exit;
    }
 
@@ -464,7 +464,7 @@
    out = std_score_Hscore(bits_cutoff,report_level);
 
    if( dbsi == NULL ) {
-      warn("Passed a NULL dbsi search implementaion object. Exiting without searching");
+      warn("Passed a NULL dbsi search implementation object. Exiting without searching");
       goto exit;
    }
 
--- a/src/dynlibsrc/translation.c
+++ b/src/dynlibsrc/translation.c
@@ -90,7 +90,7 @@
       if( i+3 >= cd->baseseq->len ) 
 	break;
       else {
-	warn("Got a stop codon in the middle of a translation at postion [%d]. Yuk!",i);
+	warn("Got a stop codon in the middle of a translation at position [%d]. Yuk!",i);
 	seq->seq[j] = '*';
       }
     } else {
--- a/src/dynlibsrc/translation.dy
+++ b/src/dynlibsrc/translation.dy
@@ -118,7 +118,7 @@
       if( i+3 >= cd->baseseq->len ) 
 	break;
       else {
-	warn("Got a stop codon in the middle of a translation at postion [%d]. Yuk!",i);
+	warn("Got a stop codon in the middle of a translation at position [%d]. Yuk!",i);
 	seq->seq[j] = '*';
       }
     } else {
--- a/src/models/phasemodel.c
+++ b/src/models/phasemodel.c
@@ -102,7 +102,7 @@
     fprintf(stdout,"for the definition of the intron. For phase 0 introns, it should be labeled as\n");
     fprintf(stdout,"the amino acid before the intron. For phase 1 and 2 introns, this is on the intron\n\n");
     fprintf(stdout,"We suggest using a small spread of positions to cope with intron positioning errors\n");
-    fprintf(stdout,"  eg, defining an intron at position 4, phase 0, make postions 3,4 and 5 with position 0\n\n");
+    fprintf(stdout,"  eg, defining an intron at position 4, phase 0, make positions 3,4 and 5 with position 0\n\n");
     fprintf(stdout,"The phase file format is\n");
     fprintf(stdout,"# lines starting with hash are comments\n");
     fprintf(stdout,"# three tab delimited columns\n");
--- a/src/models/phasemodel.dy
+++ b/src/models/phasemodel.dy
@@ -152,7 +152,7 @@
     fprintf(stdout,"for the definition of the intron. For phase 0 introns, it should be labeled as\n");
     fprintf(stdout,"the amino acid before the intron. For phase 1 and 2 introns, this is on the intron\n\n");
     fprintf(stdout,"We suggest using a small spread of positions to cope with intron positioning errors\n");
-    fprintf(stdout,"  eg, defining an intron at position 4, phase 0, make postions 3,4 and 5 with position 0\n\n");
+    fprintf(stdout,"  eg, defining an intron at position 4, phase 0, make positions 3,4 and 5 with position 0\n\n");
     fprintf(stdout,"The phase file format is\n");
     fprintf(stdout,"# lines starting with hash are comments\n");
     fprintf(stdout,"# three tab delimited columns\n");
--- a/src/models/standardout.c
+++ b/src/models/standardout.c
@@ -13,7 +13,7 @@
   fprintf(ofp,"   -alb          show align block format\n");
   fprintf(ofp,"   -pal          show raw alignment\n");
   fprintf(ofp,"   -calb         show cumlative align block\n");
-  fprintf(ofp,"   -cpal         show cumlative raw alignemnt\n");
+  fprintf(ofp,"   -cpal         show cumlative raw alignment\n");
 
 }
 
--- a/src/models/standardout.dy
+++ b/src/models/standardout.dy
@@ -27,7 +27,7 @@
   fprintf(ofp,"   -alb          show align block format\n");
   fprintf(ofp,"   -pal          show raw alignment\n");
   fprintf(ofp,"   -calb         show cumlative align block\n");
-  fprintf(ofp,"   -cpal         show cumlative raw alignemnt\n");
+  fprintf(ofp,"   -cpal         show cumlative raw alignment\n");
 
 }
 
--- a/src/dyc/method.c
+++ b/src/dyc/method.c
@@ -149,7 +149,7 @@
  *
  * Descrip:    function which handles the logical->real mapping
  *
- *             At the moment "unmappable" types get assummed to be C types,
+ *             At the moment "unmappable" types get assumed to be C types,
  *             trigger a warning and return the correct thing.
  *
  *
@@ -166,7 +166,7 @@
   Type * ty;
 
   if( (ty = Type_from_name(mts,type)) == NULL ) {
-    warn("Type [%s] is not recognised as a logical Dynamite type. Assumming it is a real C type",type);
+    warn("Type [%s] is not recognised as a logical Dynamite type. Assuming it is a real C type",type);
     return StructElement_from_nameandtype(name,type);
   }
 
--- a/src/dyc/method.dy
+++ b/src/dyc/method.dy
@@ -168,7 +168,7 @@
 %func
 function which handles the logical->real mapping
 
-At the moment "unmappable" types get assummed to be C types,
+At the moment "unmappable" types get assumed to be C types,
 trigger a warning and return the correct thing.
 %%
 StructElement * StructElement_from_MethodTypeSet(char * name,char * type,MethodTypeSet * mts)
@@ -176,7 +176,7 @@
   Type * ty;
 
   if( (ty = Type_from_name(mts,type)) == NULL ) {
-    warn("Type [%s] is not recognised as a logical Dynamite type. Assumming it is a real C type",type);
+    warn("Type [%s] is not recognised as a logical Dynamite type. Assuming it is a real C type",type);
     return StructElement_from_nameandtype(name,type);
   }
 
--- a/src/models/genewisemodel.c
+++ b/src/models/genewisemodel.c
@@ -305,7 +305,7 @@
 /* Function:  GeneWise_fold_in_synchronised_RandomModel(gw,rm,cm,*ct,stop_codon_background)
  *
  * Descrip:    This function places 'log-odd' scores of the
- *             genewise model assumming that the random model
+ *             genewise model assuming that the random model
  *             is a protein model with the codon mapper system
  *             added in, *and* that the path of the random model
  *             is synchronous with the query model.
@@ -526,7 +526,7 @@
     } else if ( strstr(col->alu[position_in_aln]->text_label,"INSERT") != NULL ) {
       continue;
     } else {
-      warn("In processing alignment to peptide, got label %s which cannot handle. Assumming X in protein translation",col->alu[position_in_aln]->text_label);
+      warn("In processing alignment to peptide, got label %s which cannot handle. Assuming X in protein translation",col->alu[position_in_aln]->text_label);
       buffer[i++] = 'X';
     }
   }
--- a/src/models/genewisemodel.dy
+++ b/src/models/genewisemodel.dy
@@ -335,7 +335,7 @@
 
 %func
 This function places 'log-odd' scores of the
-genewise model assumming that the random model
+genewise model assuming that the random model
 is a protein model with the codon mapper system
 added in, *and* that the path of the random model
 is synchronous with the query model.
@@ -516,7 +516,7 @@
     } else if ( strstr(col->alu[position_in_aln]->text_label,"INSERT") != NULL ) {
       continue;
     } else {
-      warn("In processing alignment to peptide, got label %s which cannot handle. Assumming X in protein translation",col->alu[position_in_aln]->text_label);
+      warn("In processing alignment to peptide, got label %s which cannot handle. Assuming X in protein translation",col->alu[position_in_aln]->text_label);
       buffer[i++] = 'X';
     }
   }
--- a/src/models/motifmatrix.c
+++ b/src/models/motifmatrix.c
@@ -84,7 +84,7 @@
 # line 121 "motifmatrix.dy"
 void show_help_MotifMatrixPara(FILE * ofp)
 {
-  fprintf(ofp,"Motif Matrix matching paramters\n");
+  fprintf(ofp,"Motif Matrix matching parameters\n");
   fprintf(ofp,"  -mm_motif [0.9]  Probability of a match in a motif\n");
   fprintf(ofp,"  -mm_cons  [0.75] Probability of a match in a non-motif conserved\n");
   fprintf(ofp,"  -mm_spacer[0.35] Probability of a match in a spacer\n");
--- a/src/models/motifmatrix.dy
+++ b/src/models/motifmatrix.dy
@@ -120,7 +120,7 @@
 
 void show_help_MotifMatrixPara(FILE * ofp)
 {
-  fprintf(ofp,"Motif Matrix matching paramters\n");
+  fprintf(ofp,"Motif Matrix matching parameters\n");
   fprintf(ofp,"  -mm_motif [0.9]  Probability of a match in a motif\n");
   fprintf(ofp,"  -mm_cons  [0.75] Probability of a match in a non-motif conserved\n");
   fprintf(ofp,"  -mm_spacer[0.35] Probability of a match in a spacer\n");
--- a/src/dyc/dynafunc.c
+++ b/src/dyc/dynafunc.c
@@ -983,7 +983,7 @@
 
   expr(dfp,"if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)");
   startbrace(dfp);
-  warn_expr(dfp,"Cannot iniate matrix, is not an explicit memory type and you have assummed that");
+  warn_expr(dfp,"Cannot iniate matrix, is not an explicit memory type and you have assumed that");
   expr(dfp,"return");
   closebrace(dfp);
 
@@ -1263,7 +1263,7 @@
 }
 
  /****
-   This function requires alot of stuff assummed.
+   This function requires alot of stuff assumed.
 
    int * reti, int *retj and *retstate *retspecial as parameters which will be set 
    by this block.
@@ -2020,7 +2020,7 @@
  *
  * Descrip:    This writes the special to special block movements, if needed.
  *
- *             If bestscore is not NULL, it assummes that this is the name of
+ *             If bestscore is not NULL, it assumes that this is the name of
  *             an int variable which should hold the bestscore by updating 
  *             from the end state
  *
--- a/src/dyc/dynafunc.dy
+++ b/src/dyc/dynafunc.dy
@@ -952,7 +952,7 @@
 
   expr(dfp,"if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)");
   startbrace(dfp);
-  warn_expr(dfp,"Cannot iniate matrix, is not an explicit memory type and you have assummed that");
+  warn_expr(dfp,"Cannot iniate matrix, is not an explicit memory type and you have assumed that");
   expr(dfp,"return");
   closebrace(dfp);
 
@@ -1228,7 +1228,7 @@
 }
 
  /****
-   This function requires alot of stuff assummed.
+   This function requires alot of stuff assumed.
 
    int * reti, int *retj and *retstate *retspecial as parameters which will be set 
    by this block.
@@ -1957,7 +1957,7 @@
 %func
 This writes the special to special block movements, if needed.
 
-If bestscore is not NULL, it assummes that this is the name of
+If bestscore is not NULL, it assumes that this is the name of
 an int variable which should hold the bestscore by updating 
 from the end state
 %type internal
--- a/src/dyc/method.h
+++ b/src/dyc/method.h
@@ -113,7 +113,7 @@
  *
  * Descrip:    function which handles the logical->real mapping
  *
- *             At the moment "unmappable" types get assummed to be C types,
+ *             At the moment "unmappable" types get assumed to be C types,
  *             trigger a warning and return the correct thing.
  *
  *
--- a/src/dynlibsrc/basematrix.h
+++ b/src/dynlibsrc/basematrix.h
@@ -84,7 +84,7 @@
   BASEMATRIX_TYPE_VERYSMALL
 };
 
-/* 20 MB assummed. Could break something? */
+/* 20 MB assumed. Could break something? */
 #define COMPILE_BASEMATRIX_MAX_KB 20000
 
 
--- a/src/dynlibsrc/proteinindexcons.c
+++ b/src/dynlibsrc/proteinindexcons.c
@@ -52,8 +52,8 @@
   fprintf(ofp,"   -piwaypost [number]  - waypost for streamed cases, default 3\n");
   fprintf(ofp,"   -pishadow [number]   - shadow length for shadow cases, default 15\n");
   fprintf(ofp,"   -pishadow_err [number] - errors per 100 identities tolerated, 3\n");
-  fprintf(ofp,"   -piseqmax            - indexes can assumme maximum length of seq\n");
-  fprintf(ofp,"   -piseqmax_len [number] - assummed max sequnce length, default 1000\n"); 
+  fprintf(ofp,"   -piseqmax            - indexes can assume maximum length of seq\n");
+  fprintf(ofp,"   -piseqmax_len [number] - assumed max sequnce length, default 1000\n"); 
 
   return;
 }
--- a/src/dynlibsrc/proteinindexcons.dy
+++ b/src/dynlibsrc/proteinindexcons.dy
@@ -63,8 +63,8 @@
   fprintf(ofp,"   -piwaypost [number]  - waypost for streamed cases, default 3\n");
   fprintf(ofp,"   -pishadow [number]   - shadow length for shadow cases, default 15\n");
   fprintf(ofp,"   -pishadow_err [number] - errors per 100 identities tolerated, 3\n");
-  fprintf(ofp,"   -piseqmax            - indexes can assumme maximum length of seq\n");
-  fprintf(ofp,"   -piseqmax_len [number] - assummed max sequnce length, default 1000\n"); 
+  fprintf(ofp,"   -piseqmax            - indexes can assume maximum length of seq\n");
+  fprintf(ofp,"   -piseqmax_len [number] - assumed max sequnce length, default 1000\n"); 
 
   return;
 }
--- a/src/models/alignwisedp.c
+++ b/src/models/alignwisedp.c
@@ -1214,7 +1214,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/bigdba.c
+++ b/src/models/bigdba.c
@@ -1071,7 +1071,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/clonewisedp.c
+++ b/src/models/clonewisedp.c
@@ -1040,7 +1040,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/dba.c
+++ b/src/models/dba.c
@@ -983,7 +983,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/dnaalign.c
+++ b/src/models/dnaalign.c
@@ -1077,7 +1077,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/dnaprofiledp.c
+++ b/src/models/dnaprofiledp.c
@@ -1156,7 +1156,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/editdistdp.c
+++ b/src/models/editdistdp.c
@@ -869,7 +869,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/estfrag3.c
+++ b/src/models/estfrag3.c
@@ -1129,7 +1129,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/fivestate.c
+++ b/src/models/fivestate.c
@@ -1044,7 +1044,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/genephase6.c
+++ b/src/models/genephase6.c
@@ -1653,7 +1653,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/genomewise9.c
+++ b/src/models/genomewise9.c
@@ -1501,7 +1501,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/largeblockdp.c
+++ b/src/models/largeblockdp.c
@@ -844,7 +844,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/localclonewisedp.c
+++ b/src/models/localclonewisedp.c
@@ -960,7 +960,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/localdba.c
+++ b/src/models/localdba.c
@@ -999,7 +999,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/motifmatrixdp.c
+++ b/src/models/motifmatrixdp.c
@@ -772,7 +772,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/slimdba.c
+++ b/src/models/slimdba.c
@@ -761,7 +761,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/statwise10.c
+++ b/src/models/statwise10.c
@@ -580,7 +580,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/sw_wrap.c
+++ b/src/models/sw_wrap.c
@@ -333,7 +333,7 @@
 /* Function:  Align_Proteins_SmithWaterman(one,two,comp,gap,ext,dpenv,dpri)
  *
  * Descrip:    This is the most correct way of aligning two Proteins,
- *             using Protein objects, which can be assummed to be
+ *             using Protein objects, which can be assumed to be
  *             proteins with no objections
  *
  *             To display the alignment use write_pretty_Protein_align
@@ -394,7 +394,7 @@
    out = std_score_Hscore(bits_cutoff,report_level);
 
    if( dbsi == NULL ) {
-      warn("Passed a NULL dbsi search implementaion object. Exiting without searching");
+      warn("Passed a NULL dbsi search implementation object. Exiting without searching");
       goto exit;
    }
 
@@ -452,7 +452,7 @@
    out = std_score_Hscore(bits_cutoff,report_level);
 
    if( dbsi == NULL ) {
-      warn("Passed a NULL dbsi search implementaion object. Exiting without searching");
+      warn("Passed a NULL dbsi search implementation object. Exiting without searching");
       goto exit;
    }
 
@@ -511,7 +511,7 @@
    out = std_score_Hscore(bits_cutoff,report_level);
 
    if( dbsi == NULL ) {
-      warn("Passed a NULL dbsi search implementaion object. Exiting without searching");
+      warn("Passed a NULL dbsi search implementation object. Exiting without searching");
       goto exit;
    }
 
--- a/src/models/sw_wrap.h
+++ b/src/models/sw_wrap.h
@@ -144,7 +144,7 @@
 /* Function:  Align_Proteins_SmithWaterman(one,two,comp,gap,ext,dpenv,dpri)
  *
  * Descrip:    This is the most correct way of aligning two Proteins,
- *             using Protein objects, which can be assummed to be
+ *             using Protein objects, which can be assumed to be
  *             proteins with no objections
  *
  *             To display the alignment use write_pretty_Protein_align
--- a/src/models/sw_wrap.pod
+++ b/src/models/sw_wrap.pod
@@ -67,7 +67,7 @@
 &Wise2::Align_Proteins_SmithWaterman(one,two,comp,gap,ext,dpenv,dpri)
 
   This is the most correct way of aligning two Proteins,
-  using Protein objects, which can be assummed to be
+  using Protein objects, which can be assumed to be
   proteins with no objections
 
   To display the alignment use write_pretty_Protein_align
--- a/src/models/sw_wrap.tex
+++ b/src/models/sw_wrap.tex
@@ -80,7 +80,7 @@
 \item[returns] [UNKN ] Undocumented return value [AlnBlock *]
 \end{description}
 This is the most correct way of aligning two Proteins,
-using Protein objects, which can be assummed to be
+using Protein objects, which can be assumed to be
 proteins with no objections
 
 
--- a/src/models/sw_wrap_api.h
+++ b/src/models/sw_wrap_api.h
@@ -70,7 +70,7 @@
 /* Function:  Wise2_Align_Proteins_SmithWaterman(one,two,comp,gap,ext,dpenv,dpri)
  *
  * Descrip:    This is the most correct way of aligning two Proteins,
- *             using Protein objects, which can be assummed to be
+ *             using Protein objects, which can be assumed to be
  *             proteins with no objections
  *
  *             To display the alignment use write_pretty_Protein_align
--- a/src/models/sywise20.c
+++ b/src/models/sywise20.c
@@ -1531,7 +1531,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/threestatedp.c
+++ b/src/models/threestatedp.c
@@ -864,7 +864,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/threestateloop.c
+++ b/src/models/threestateloop.c
@@ -950,7 +950,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/models/transregiondp.c
+++ b/src/models/transregiondp.c
@@ -1008,7 +1008,7 @@
     register int i;  
     register int j;  
     if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)   {  
-      warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");   
+      warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");   
       return;    
       }  
 
--- a/src/dyc/dynashadow.c
+++ b/src/dyc/dynashadow.c
@@ -2438,7 +2438,7 @@
   register int j;
   register int k;
 
-  /*** this function assummes the following local variables
+  /*** this function assumes the following local variables
 
     int score
     int temp
--- a/src/dyc/dynashadow.dy
+++ b/src/dyc/dynashadow.dy
@@ -2358,7 +2358,7 @@
   register int j;
   register int k;
 
-  /*** this function assummes the following local variables
+  /*** this function assumes the following local variables
 
     int score
     int temp
--- a/src/dynlibsrc/aln.c
+++ b/src/dynlibsrc/aln.c
@@ -67,7 +67,7 @@
 
 /* Function:  add_to_anchored_AlnBlock(growing,add)
  *
- * Descrip:    This function assummes that the first AlnSequence
+ * Descrip:    This function assumes that the first AlnSequence
  *             in the current and the adding AlnBlock are the same,
  *             and that you want to add the second AlnSequence of the
  *             second alnblock to the first, anchored on the first
--- a/src/dynlibsrc/aln.dy
+++ b/src/dynlibsrc/aln.dy
@@ -157,7 +157,7 @@
 }
 
 %func
-This function assummes that the first AlnSequence
+This function assumes that the first AlnSequence
 in the current and the adding AlnBlock are the same,
 and that you want to add the second AlnSequence of the
 second alnblock to the first, anchored on the first
--- a/src/dynlibsrc/aln.h
+++ b/src/dynlibsrc/aln.h
@@ -198,7 +198,7 @@
 
 /* Function:  add_to_anchored_AlnBlock(growing,add)
  *
- * Descrip:    This function assummes that the first AlnSequence
+ * Descrip:    This function assumes that the first AlnSequence
  *             in the current and the adding AlnBlock are the same,
  *             and that you want to add the second AlnSequence of the
  *             second alnblock to the first, anchored on the first
--- a/src/dynlibsrc/codon.c
+++ b/src/dynlibsrc/codon.c
@@ -486,7 +486,7 @@
  *
  * Descrip:    takes an ASCII coded pointer to a 3 base pair
  *             sequence (it could be the part of a sequence: it only
- *             assummes that the seq points with 3 chars at pos 0,1,2 
+ *             assumes that the seq points with 3 chars at pos 0,1,2 
  *             in C coordinates from seq. No NULL is required). It 
  *             ives back the codon as made from standard mapping, ie,
  *             25*base_1+5*base_2 + base3 being a number from 0-124 inc.
--- a/src/dynlibsrc/codon.dy
+++ b/src/dynlibsrc/codon.dy
@@ -451,7 +451,7 @@
 %func
 takes an ASCII coded pointer to a 3 base pair
 sequence (it could be the part of a sequence: it only
-assummes that the seq points with 3 chars at pos 0,1,2 
+assumes that the seq points with 3 chars at pos 0,1,2 
 in C coordinates from seq. No NULL is required). It 
 ives back the codon as made from standard mapping, ie,
 25*base_1+5*base_2 + base3 being a number from 0-124 inc.
--- a/src/dynlibsrc/codon.h
+++ b/src/dynlibsrc/codon.h
@@ -324,7 +324,7 @@
  *
  * Descrip:    takes an ASCII coded pointer to a 3 base pair
  *             sequence (it could be the part of a sequence: it only
- *             assummes that the seq points with 3 chars at pos 0,1,2 
+ *             assumes that the seq points with 3 chars at pos 0,1,2 
  *             in C coordinates from seq. No NULL is required). It 
  *             ives back the codon as made from standard mapping, ie,
  *             25*base_1+5*base_2 + base3 being a number from 0-124 inc.
--- a/src/dynlibsrc/codon.pod
+++ b/src/dynlibsrc/codon.pod
@@ -282,7 +282,7 @@
 
   takes an ASCII coded pointer to a 3 base pair
   sequence (it could be the part of a sequence: it only
-  assummes that the seq points with 3 chars at pos 0,1,2 
+  assumes that the seq points with 3 chars at pos 0,1,2 
   in C coordinates from seq. No NULL is required). It 
   ives back the codon as made from standard mapping, ie,
   25*base_1+5*base_2 + base3 being a number from 0-124 inc.
--- a/src/dynlibsrc/codon.tex
+++ b/src/dynlibsrc/codon.tex
@@ -121,7 +121,7 @@
 \end{description}
 takes an ASCII coded pointer to a 3 base pair
 sequence (it could be the part of a sequence: it only
-assummes that the seq points with 3 chars at pos 0,1,2 
+assumes that the seq points with 3 chars at pos 0,1,2 
 in C coordinates from seq. No NULL is required). It 
 ives back the codon as made from standard mapping, ie,
 25*base_1+5*base_2 + base3 being a number from 0-124 inc.
--- a/src/dynlibsrc/codon_api.h
+++ b/src/dynlibsrc/codon_api.h
@@ -279,7 +279,7 @@
  *
  * Descrip:    takes an ASCII coded pointer to a 3 base pair
  *             sequence (it could be the part of a sequence: it only
- *             assummes that the seq points with 3 chars at pos 0,1,2 
+ *             assumes that the seq points with 3 chars at pos 0,1,2 
  *             in C coordinates from seq. No NULL is required). It 
  *             ives back the codon as made from standard mapping, ie,
  *             25*base_1+5*base_2 + base3 being a number from 0-124 inc.
--- a/src/dynlibsrc/codonmapper.c
+++ b/src/dynlibsrc/codonmapper.c
@@ -285,7 +285,7 @@
 
 /* Function:  sprinkle_errors_over_CodonMapper(cm,error)
  *
- * Descrip:    Takes a codon mapper and assummes that the majority of errors
+ * Descrip:    Takes a codon mapper and assumes that the majority of errors
  *             are due to a single base change in the codon at probability error.
  *             Therefore, for each codon it adds error * prob(codon) * 0.25 to each 
  *             other codon one base away, taking away therefore the result.
--- a/src/dynlibsrc/codonmapper.dy
+++ b/src/dynlibsrc/codonmapper.dy
@@ -271,7 +271,7 @@
 }
 
 %func
-Takes a codon mapper and assummes that the majority of errors
+Takes a codon mapper and assumes that the majority of errors
 are due to a single base change in the codon at probability error.
 Therefore, for each codon it adds error * prob(codon) * 0.25 to each 
 other codon one base away, taking away therefore the result.
--- a/src/dynlibsrc/codonmapper.h
+++ b/src/dynlibsrc/codonmapper.h
@@ -165,7 +165,7 @@
 
 /* Function:  sprinkle_errors_over_CodonMapper(cm,error)
  *
- * Descrip:    Takes a codon mapper and assummes that the majority of errors
+ * Descrip:    Takes a codon mapper and assumes that the majority of errors
  *             are due to a single base change in the codon at probability error.
  *             Therefore, for each codon it adds error * prob(codon) * 0.25 to each 
  *             other codon one base away, taking away therefore the result.
--- a/src/dynlibsrc/codonmapper.pod
+++ b/src/dynlibsrc/codonmapper.pod
@@ -50,7 +50,7 @@
 
 &Wise2::CodonMapper::sprinkle_errors_over_CodonMapper(cm,error)
 
-  Takes a codon mapper and assummes that the majority of errors
+  Takes a codon mapper and assumes that the majority of errors
   are due to a single base change in the codon at probability error.
   Therefore, for each codon it adds error * prob(codon) * 0.25 to each 
   other codon one base away, taking away therefore the result.
--- a/src/dynlibsrc/codonmapper.tex
+++ b/src/dynlibsrc/codonmapper.tex
@@ -69,7 +69,7 @@
 \item[error] [UNKN ] substitution error rate [double]
 \item[returns] Nothing - no return value
 \end{description}
-Takes a codon mapper and assummes that the majority of errors
+Takes a codon mapper and assumes that the majority of errors
 are due to a single base change in the codon at probability error.
 Therefore, for each codon it adds error * prob(codon) * 0.25 to each 
 other codon one base away, taking away therefore the result.
--- a/src/dynlibsrc/codonmapper_api.h
+++ b/src/dynlibsrc/codonmapper_api.h
@@ -21,7 +21,7 @@
 /* API for object CodonMapper */
 /* Function:  Wise2_sprinkle_errors_over_CodonMapper(cm,error)
  *
- * Descrip:    Takes a codon mapper and assummes that the majority of errors
+ * Descrip:    Takes a codon mapper and assumes that the majority of errors
  *             are due to a single base change in the codon at probability error.
  *             Therefore, for each codon it adds error * prob(codon) * 0.25 to each 
  *             other codon one base away, taking away therefore the result.
--- a/src/dynlibsrc/codonmatrix.c
+++ b/src/dynlibsrc/codonmatrix.c
@@ -100,7 +100,7 @@
 
 /* Function:  naive_CodonMatrixScore(ct,comp)
  *
- * Descrip:    Builds a codon matrix from CompMat which assummes:
+ * Descrip:    Builds a codon matrix from CompMat which assumes:
  *               No codon Bias
  *               No errors
  *             N codons score 0, stop codons score ??
--- a/src/dynlibsrc/codonmatrix.dy
+++ b/src/dynlibsrc/codonmatrix.dy
@@ -85,7 +85,7 @@
 
 
 %func
-Builds a codon matrix from CompMat which assummes:
+Builds a codon matrix from CompMat which assumes:
   No codon Bias
   No errors
 N codons score 0, stop codons score ??
--- a/src/dynlibsrc/codonmatrix.h
+++ b/src/dynlibsrc/codonmatrix.h
@@ -94,7 +94,7 @@
 
 /* Function:  naive_CodonMatrixScore(ct,comp)
  *
- * Descrip:    Builds a codon matrix from CompMat which assummes:
+ * Descrip:    Builds a codon matrix from CompMat which assumes:
  *               No codon Bias
  *               No errors
  *             N codons score 0, stop codons score ??
--- a/src/dynlibsrc/genomic.c
+++ b/src/dynlibsrc/genomic.c
@@ -103,7 +103,7 @@
 
 /* Function:  read_fasta_file_Genomic(filename,length_of_N)
  *
- * Descrip:    Reads a fasta file assumming that it is Genomic. 
+ * Descrip:    Reads a fasta file assuming that it is Genomic. 
  *             Will complain if it is not, and return NULL.
  *
  *
@@ -135,7 +135,7 @@
 
 /* Function:  read_fasta_Genomic(ifp,length_of_N)
  *
- * Descrip:    Reads a fasta file assumming that it is Genomic. 
+ * Descrip:    Reads a fasta file assuming that it is Genomic. 
  *             Will complain if it is not, and return NULL.
  *
  *
@@ -216,7 +216,7 @@
 /* Function:  Genomic_from_Sequence_Nheuristic(seq,length_of_N)
  *
  * Descrip:    makes a new genomic from a Sequence, but
- *             assummes that all the N runs greater than
+ *             assumes that all the N runs greater than
  *             a certain level are actually repeats.
  *
  *
--- a/src/dynlibsrc/genomic.dy
+++ b/src/dynlibsrc/genomic.dy
@@ -129,7 +129,7 @@
 
 
 %func
-Reads a fasta file assumming that it is Genomic. 
+Reads a fasta file assuming that it is Genomic. 
 Will complain if it is not, and return NULL.
 %arg
 filename filename to be opened and read
@@ -155,7 +155,7 @@
 
 
 %func
-Reads a fasta file assumming that it is Genomic. 
+Reads a fasta file assuming that it is Genomic. 
 Will complain if it is not, and return NULL.
 %arg
 ifp file point to be read from
@@ -210,7 +210,7 @@
 
 %func
 makes a new genomic from a Sequence, but
-assummes that all the N runs greater than
+assumes that all the N runs greater than
 a certain level are actually repeats.
 %%
 Genomic * Genomic_from_Sequence_Nheuristic(Sequence * seq,int length_of_N)
--- a/src/dynlibsrc/genomic.h
+++ b/src/dynlibsrc/genomic.h
@@ -91,7 +91,7 @@
 
 /* Function:  read_fasta_file_Genomic(filename,length_of_N)
  *
- * Descrip:    Reads a fasta file assumming that it is Genomic. 
+ * Descrip:    Reads a fasta file assuming that it is Genomic. 
  *             Will complain if it is not, and return NULL.
  *
  *
@@ -107,7 +107,7 @@
 
 /* Function:  read_fasta_Genomic(ifp,length_of_N)
  *
- * Descrip:    Reads a fasta file assumming that it is Genomic. 
+ * Descrip:    Reads a fasta file assuming that it is Genomic. 
  *             Will complain if it is not, and return NULL.
  *
  *
@@ -167,7 +167,7 @@
 /* Function:  Genomic_from_Sequence_Nheuristic(seq,length_of_N)
  *
  * Descrip:    makes a new genomic from a Sequence, but
- *             assummes that all the N runs greater than
+ *             assumes that all the N runs greater than
  *             a certain level are actually repeats.
  *
  *
--- a/src/dynlibsrc/genomic.pod
+++ b/src/dynlibsrc/genomic.pod
@@ -355,7 +355,7 @@
 
 &Wise2::read_fasta_file_Genomic(filename,length_of_N)
 
-  Reads a fasta file assumming that it is Genomic. 
+  Reads a fasta file assuming that it is Genomic. 
   Will complain if it is not, and return NULL.
 
 
@@ -369,7 +369,7 @@
 
 &Wise2::read_fasta_Genomic(ifp,length_of_N)
 
-  Reads a fasta file assumming that it is Genomic. 
+  Reads a fasta file assuming that it is Genomic. 
   Will complain if it is not, and return NULL.
 
 
@@ -384,7 +384,7 @@
 &Wise2::Genomic_from_Sequence_Nheuristic(seq,length_of_N)
 
   makes a new genomic from a Sequence, but
-  assummes that all the N runs greater than
+  assumes that all the N runs greater than
   a certain level are actually repeats.
 
 
--- a/src/dynlibsrc/genomic.tex
+++ b/src/dynlibsrc/genomic.tex
@@ -22,7 +22,7 @@
 \item[length_of_N] [UNKN ] length of N to be considered repeat. -1 means none [int]
 \item[returns] [UNKN ] Undocumented return value [Genomic *]
 \end{description}
-Reads a fasta file assumming that it is Genomic. 
+Reads a fasta file assuming that it is Genomic. 
 Will complain if it is not, and return NULL.
 
 
@@ -38,7 +38,7 @@
 \item[length_of_N] [UNKN ] length of N to be considered repeat. -1 means none [int]
 \item[returns] [UNKN ] Undocumented return value [Genomic *]
 \end{description}
-Reads a fasta file assumming that it is Genomic. 
+Reads a fasta file assuming that it is Genomic. 
 Will complain if it is not, and return NULL.
 
 
@@ -55,7 +55,7 @@
 \item[returns] [UNKN ] Undocumented return value [Genomic *]
 \end{description}
 makes a new genomic from a Sequence, but
-assummes that all the N runs greater than
+assumes that all the N runs greater than
 a certain level are actually repeats.
 
 
--- a/src/dynlibsrc/genomic_api.h
+++ b/src/dynlibsrc/genomic_api.h
@@ -360,7 +360,7 @@
 /* These functions are not associated with an object */
 /* Function:  Wise2_read_fasta_file_Genomic(filename,length_of_N)
  *
- * Descrip:    Reads a fasta file assumming that it is Genomic. 
+ * Descrip:    Reads a fasta file assuming that it is Genomic. 
  *             Will complain if it is not, and return NULL.
  *
  *
@@ -374,7 +374,7 @@
 
 /* Function:  Wise2_read_fasta_Genomic(ifp,length_of_N)
  *
- * Descrip:    Reads a fasta file assumming that it is Genomic. 
+ * Descrip:    Reads a fasta file assuming that it is Genomic. 
  *             Will complain if it is not, and return NULL.
  *
  *
@@ -389,7 +389,7 @@
 /* Function:  Wise2_Genomic_from_Sequence_Nheuristic(seq,length_of_N)
  *
  * Descrip:    makes a new genomic from a Sequence, but
- *             assummes that all the N runs greater than
+ *             assumes that all the N runs greater than
  *             a certain level are actually repeats.
  *
  *
--- a/src/dynlibsrc/hspstream.c
+++ b/src/dynlibsrc/hspstream.c
@@ -38,7 +38,7 @@
   SequenceSet * out;
   char buffer[512];
 
-  /* assumme that each HSPset has only one target sequence */
+  /* assume that each HSPset has only one target sequence */
 
   out = SequenceSet_alloc_len(lm->len+1);  
 
@@ -109,7 +109,7 @@
  *
  * Descrip:    typed linear hsp manager from stream
  *
- *             assummes sequences coming in first, with query as first sequence
+ *             assumes sequences coming in first, with query as first sequence
  *             and then hsps one after the other
  *
  *
--- a/src/dynlibsrc/hspstream.dy
+++ b/src/dynlibsrc/hspstream.dy
@@ -31,7 +31,7 @@
   SequenceSet * out;
   char buffer[512];
 
-  /* assumme that each HSPset has only one target sequence */
+  /* assume that each HSPset has only one target sequence */
 
   out = SequenceSet_alloc_len(lm->len+1);  
 
@@ -93,7 +93,7 @@
 %func
 typed linear hsp manager from stream
 
-assummes sequences coming in first, with query as first sequence
+assumes sequences coming in first, with query as first sequence
 and then hsps one after the other
 %%
 LinearHSPmanager * typed_LinearHSPmanager_from_Stream(Wise2ReadStreamInterface * rs)
--- a/src/dynlibsrc/hspstream.h
+++ b/src/dynlibsrc/hspstream.h
@@ -64,7 +64,7 @@
  *
  * Descrip:    typed linear hsp manager from stream
  *
- *             assummes sequences coming in first, with query as first sequence
+ *             assumes sequences coming in first, with query as first sequence
  *             and then hsps one after the other
  *
  *
--- a/src/dynlibsrc/sequence.c
+++ b/src/dynlibsrc/sequence.c
@@ -296,7 +296,7 @@
 /* Function:  translate_Sequence(dna,ct)
  *
  * Descrip:    This translates a DNA sequence to a protein.
- *             It assummes that it starts at first residue
+ *             It assumes that it starts at first residue
  *             (use trunc_Sequence to chop a sequence up).
  *
  *
@@ -600,7 +600,7 @@
  * Descrip:    reads efetch specificed sequence. calls popen to
  *             efetch. A hack around accession numbers so that if the 
  *             thing looks like WP:acc number, calls it with -a...
- *             otherwise assummes you have both database and name in the
+ *             otherwise assumes you have both database and name in the
  *             efetchstring
  *
  *
@@ -746,7 +746,7 @@
 
 /* Function:  read_fasta_Sequence(ifp)
  *
- * Descrip:    reads a fasta file assumming pretty 
+ * Descrip:    reads a fasta file assuming pretty 
  *             standard sanity for the file layout
  *
  *
@@ -806,7 +806,7 @@
   }
   
   if( buffer[0] != '>' ) {
-    warn("First character read not >, assumming is not fasta");
+    warn("First character read not >, assuming is not fasta");
     return NULL;
   }
 
@@ -933,7 +933,7 @@
     return NULL;
 
   if( c != '>' ) {
-    warn("First letter read is not '>' - assumming it is not a fasta stream");
+    warn("First letter read is not '>' - assuming it is not a fasta stream");
     return NULL;
   }
 
--- a/src/dynlibsrc/sequence.h
+++ b/src/dynlibsrc/sequence.h
@@ -260,7 +260,7 @@
 /* Function:  translate_Sequence(dna,ct)
  *
  * Descrip:    This translates a DNA sequence to a protein.
- *             It assummes that it starts at first residue
+ *             It assumes that it starts at first residue
  *             (use trunc_Sequence to chop a sequence up).
  *
  *
@@ -407,7 +407,7 @@
  * Descrip:    reads efetch specificed sequence. calls popen to
  *             efetch. A hack around accession numbers so that if the 
  *             thing looks like WP:acc number, calls it with -a...
- *             otherwise assummes you have both database and name in the
+ *             otherwise assumes you have both database and name in the
  *             efetchstring
  *
  *
@@ -459,7 +459,7 @@
 
 /* Function:  read_fasta_Sequence(ifp)
  *
- * Descrip:    reads a fasta file assumming pretty 
+ * Descrip:    reads a fasta file assuming pretty 
  *             standard sanity for the file layout
  *
  *
--- a/src/dynlibsrc/sequence.pod
+++ b/src/dynlibsrc/sequence.pod
@@ -136,7 +136,7 @@
 &Wise2::Sequence::translate(dna,ct)
 
   This translates a DNA sequence to a protein.
-  It assummes that it starts at first residue
+  It assumes that it starts at first residue
   (use trunc_Sequence to chop a sequence up).
 
 
@@ -267,7 +267,7 @@
 
 &Wise2::Sequence::read_fasta_Sequence(ifp)
 
-  reads a fasta file assumming pretty 
+  reads a fasta file assuming pretty 
   standard sanity for the file layout
 
 
--- a/src/dynlibsrc/sequence.tex
+++ b/src/dynlibsrc/sequence.tex
@@ -196,7 +196,7 @@
 \item[returns] [OWNER] new protein sequence [Sequence *]
 \end{description}
 This translates a DNA sequence to a protein.
-It assummes that it starts at first residue
+It assumes that it starts at first residue
 (use trunc_Sequence to chop a sequence up).
 
 
@@ -384,7 +384,7 @@
 \item[ifp] [UNKN ] Undocumented argument [FILE *]
 \item[returns] [UNKN ] Undocumented return value [Sequence *]
 \end{description}
-reads a fasta file assumming pretty 
+reads a fasta file assuming pretty 
 standard sanity for the file layout
 
 
--- a/src/dynlibsrc/sequence_api.h
+++ b/src/dynlibsrc/sequence_api.h
@@ -118,7 +118,7 @@
 /* Function:  Wise2_translate_Sequence(dna,ct)
  *
  * Descrip:    This translates a DNA sequence to a protein.
- *             It assummes that it starts at first residue
+ *             It assumes that it starts at first residue
  *             (use trunc_Sequence to chop a sequence up).
  *
  *
@@ -249,7 +249,7 @@
 
 /* Function:  Wise2_read_fasta_Sequence(ifp)
  *
- * Descrip:    reads a fasta file assumming pretty 
+ * Descrip:    reads a fasta file assuming pretty 
  *             standard sanity for the file layout
  *
  *
--- a/src/dynlibsrc/sequence_codon.c
+++ b/src/dynlibsrc/sequence_codon.c
@@ -106,7 +106,7 @@
 /* Function:  translate_Sequence(dna,ct)
  *
  * Descrip:    This translates a DNA sequence to a protein.
- *             It assummes that it starts at first residue
+ *             It assumes that it starts at first residue
  *             (use trunc_Sequence to chop a sequence up).
  *
  *
--- a/src/dynlibsrc/sequence_codon.dy
+++ b/src/dynlibsrc/sequence_codon.dy
@@ -108,7 +108,7 @@
 
 %func
 This translates a DNA sequence to a protein.
-It assummes that it starts at first residue
+It assumes that it starts at first residue
 (use trunc_Sequence to chop a sequence up).
 %simple translate
 %arg
--- a/src/dynlibsrc/sequence_codon.h
+++ b/src/dynlibsrc/sequence_codon.h
@@ -62,7 +62,7 @@
 /* Function:  translate_Sequence(dna,ct)
  *
  * Descrip:    This translates a DNA sequence to a protein.
- *             It assummes that it starts at first residue
+ *             It assumes that it starts at first residue
  *             (use trunc_Sequence to chop a sequence up).
  *
  *
--- a/src/dynlibsrc/sequence_codon.pod
+++ b/src/dynlibsrc/sequence_codon.pod
@@ -54,7 +54,7 @@
 &Wise2::translate(dna,ct)
 
   This translates a DNA sequence to a protein.
-  It assummes that it starts at first residue
+  It assumes that it starts at first residue
   (use trunc_Sequence to chop a sequence up).
 
 
--- a/src/dynlibsrc/sequence_codon.tex
+++ b/src/dynlibsrc/sequence_codon.tex
@@ -63,7 +63,7 @@
 \item[returns] [OWNER] new protein sequence [Sequence *]
 \end{description}
 This translates a DNA sequence to a protein.
-It assummes that it starts at first residue
+It assumes that it starts at first residue
 (use trunc_Sequence to chop a sequence up).
 
 
--- a/src/dynlibsrc/sequence_codon_api.h
+++ b/src/dynlibsrc/sequence_codon_api.h
@@ -52,7 +52,7 @@
 /* Function:  Wise2_translate_Sequence(dna,ct)
  *
  * Descrip:    This translates a DNA sequence to a protein.
- *             It assummes that it starts at first residue
+ *             It assumes that it starts at first residue
  *             (use trunc_Sequence to chop a sequence up).
  *
  *
--- a/src/models/genefrequency.h
+++ b/src/models/genefrequency.h
@@ -260,7 +260,7 @@
 
 /* Function:  read_base_GeneConsensus(base_array,line,ifp)
  *
- * Descrip:    assummes base_array is 4 positions long
+ * Descrip:    assumes base_array is 4 positions long
  *               
  *             line should have begin consensus on it and be of MAXLINE length as it will be used as the buffer.
  *               
@@ -280,7 +280,7 @@
 
 /* Function:  read_codon_GeneConsensus(codon_array,line,ifp)
  *
- * Descrip:    assummes codon_array is 64 positions long
+ * Descrip:    assumes codon_array is 64 positions long
  *               
  *             line should have begin consensus on it and be of MAXLINE length as it will be used as the buffer.
  *
--- a/src/models/genestats.c
+++ b/src/models/genestats.c
@@ -899,7 +899,7 @@
 
 /* Function:  read_codon_GeneStats(codon_array,line,ifp)
  *
- * Descrip:    assummes codon_array is 64 positions long
+ * Descrip:    assumes codon_array is 64 positions long
  *               
  *             line should have begin consensus on it and be of MAXLINE length as it will be used as the buffer.
  *
--- a/src/models/genestats.dy
+++ b/src/models/genestats.dy
@@ -810,7 +810,7 @@
 
 
 %func
-assummes codon_array is 64 positions long
+assumes codon_array is 64 positions long
   
 line should have begin consensus on it and be of MAXLINE length as it will be used as the buffer.
 
--- a/src/models/genestats.h
+++ b/src/models/genestats.h
@@ -380,7 +380,7 @@
 
 /* Function:  read_codon_GeneStats(codon_array,line,ifp)
  *
- * Descrip:    assummes codon_array is 64 positions long
+ * Descrip:    assumes codon_array is 64 positions long
  *               
  *             line should have begin consensus on it and be of MAXLINE length as it will be used as the buffer.
  *
--- a/src/perl/scripts/blastwise.pl
+++ b/src/perl/scripts/blastwise.pl
@@ -20,7 +20,7 @@
 site: I cant second guess all the things you want to do with the
 output, so you give it a go.
 
-This assummes that the database you are searching *is* swissprot and
+This assumes that the database you are searching *is* swissprot and
 you have SRS indexed it into the database called swissprot.  If you
 are running it on different database with a different indexer you will
 need to change the executable used to retrieve the sequence
--- a/src/dyc/api.c
+++ b/src/dyc/api.c
@@ -957,7 +957,7 @@
     if( fu->fi->ret->argtype == ARGTYPE_STATIC && is_basic_type_API(fu->fi->ret->type) == FALSE) {
       /* we need to put in the memory handler... */
       /*
-       * Horrible hack. We assumme the the C type MyType * means dynamite type MyType.
+       * Horrible hack. We assume the the C type MyType * means dynamite type MyType.
        *
        * YUK!!!! Also - v.v.v.v.v bad hard coded Wise2
        *
--- a/src/dyc/api.dy
+++ b/src/dyc/api.dy
@@ -973,7 +973,7 @@
     if( fu->fi->ret->argtype == ARGTYPE_STATIC && is_basic_type_API(fu->fi->ret->type) == FALSE) {
       /* we need to put in the memory handler... */
       /*
-       * Horrible hack. We assumme the the C type MyType * means dynamite type MyType.
+       * Horrible hack. We assume the the C type MyType * means dynamite type MyType.
        *
        * YUK!!!! Also - v.v.v.v.v bad hard coded Wise2
        *
--- a/src/dyc/funcinfo.c
+++ b/src/dyc/funcinfo.c
@@ -271,7 +271,7 @@
 
     ***/
 
-  /** assumme type (*name)(type,type,type) ***/
+  /** assume type (*name)(type,type,type) ***/
 
   held = stringalloc(str);
 
--- a/src/dyc/funcinfo.dy
+++ b/src/dyc/funcinfo.dy
@@ -318,7 +318,7 @@
 
     ***/
 
-  /** assumme type (*name)(type,type,type) ***/
+  /** assume type (*name)(type,type,type) ***/
 
   held = stringalloc(str);
 
--- a/src/dynlibsrc/genomicdb.c
+++ b/src/dynlibsrc/genomicdb.c
@@ -63,7 +63,7 @@
     warn("Cannot get entry for %s from Genomic db",de->name);
   }
 
-  /* check dna status. We assumme someone knows what he is doing when he makes a genomic db!*/
+  /* check dna status. We assume someone knows what he is doing when he makes a genomic db!*/
   if( seq->type != SEQUENCE_DNA) {
     warn("Sequence from %s data entry doesn't look like DNA. Forcing it to",de->name);
   }
@@ -142,7 +142,7 @@
     return NULL; 
   }
 
-  /* check dna status. We assumme someone knows what he is doing when he makes a genomic db!*/
+  /* check dna status. We assume someone knows what he is doing when he makes a genomic db!*/
   if( seq->type != SEQUENCE_DNA) {
     warn("Sequence from %s data entry doesn't look like DNA. Forcing it to",seq->name);
   }
@@ -247,7 +247,7 @@
 
   uppercase_Sequence(seq);
 
-  /* check dna status. We assumme someone knows what he is doing when he makes a genomic db!*/
+  /* check dna status. We assume someone knows what he is doing when he makes a genomic db!*/
   if( seq->type != SEQUENCE_DNA) {
     warn("Sequence from %s data entry doesn't look like DNA. Forcing it to",seq->name);
   }
--- a/src/dynlibsrc/genomicdb.dy
+++ b/src/dynlibsrc/genomicdb.dy
@@ -112,7 +112,7 @@
     warn("Cannot get entry for %s from Genomic db",de->name);
   }
 
-  /* check dna status. We assumme someone knows what he is doing when he makes a genomic db!*/
+  /* check dna status. We assume someone knows what he is doing when he makes a genomic db!*/
   if( seq->type != SEQUENCE_DNA) {
     warn("Sequence from %s data entry doesn't look like DNA. Forcing it to",de->name);
   }
@@ -175,7 +175,7 @@
     return NULL; 
   }
 
-  /* check dna status. We assumme someone knows what he is doing when he makes a genomic db!*/
+  /* check dna status. We assume someone knows what he is doing when he makes a genomic db!*/
   if( seq->type != SEQUENCE_DNA) {
     warn("Sequence from %s data entry doesn't look like DNA. Forcing it to",seq->name);
   }
@@ -273,7 +273,7 @@
 
   uppercase_Sequence(seq);
 
-  /* check dna status. We assumme someone knows what he is doing when he makes a genomic db!*/
+  /* check dna status. We assume someone knows what he is doing when he makes a genomic db!*/
   if( seq->type != SEQUENCE_DNA) {
     warn("Sequence from %s data entry doesn't look like DNA. Forcing it to",seq->name);
   }
--- a/src/dynlibsrc/genomicregion.c
+++ b/src/dynlibsrc/genomicregion.c
@@ -975,7 +975,7 @@
 
 /* Function:  write_Embl_FT_GenomicRegion(gr,ofp)
  *
- * Descrip:    Writes Embl feature table. Does assumme that
+ * Descrip:    Writes Embl feature table. Does assume that
  *             there is only one transcript per gene and only
  *             cds exons are used
  *
@@ -1008,7 +1008,7 @@
 
 /* Function:  write_Diana_FT_GenomicRegion(gr,ofp)
  *
- * Descrip:    Writes Embl feature table for diana use. Does assumme that
+ * Descrip:    Writes Embl feature table for diana use. Does assume that
  *             there is only one transcript per gene and only
  *             cds exons are used
  *
--- a/src/dynlibsrc/genomicregion.dy
+++ b/src/dynlibsrc/genomicregion.dy
@@ -847,7 +847,7 @@
 }
 
 %func
-Writes Embl feature table. Does assumme that
+Writes Embl feature table. Does assume that
 there is only one transcript per gene and only
 cds exons are used
 
@@ -873,7 +873,7 @@
 }
 
 %func
-Writes Embl feature table for diana use. Does assumme that
+Writes Embl feature table for diana use. Does assume that
 there is only one transcript per gene and only
 cds exons are used
 
--- a/src/dynlibsrc/genomicregion.h
+++ b/src/dynlibsrc/genomicregion.h
@@ -455,7 +455,7 @@
 
 /* Function:  write_Embl_FT_GenomicRegion(gr,ofp)
  *
- * Descrip:    Writes Embl feature table. Does assumme that
+ * Descrip:    Writes Embl feature table. Does assume that
  *             there is only one transcript per gene and only
  *             cds exons are used
  *
@@ -474,7 +474,7 @@
 
 /* Function:  write_Diana_FT_GenomicRegion(gr,ofp)
  *
- * Descrip:    Writes Embl feature table for diana use. Does assumme that
+ * Descrip:    Writes Embl feature table for diana use. Does assume that
  *             there is only one transcript per gene and only
  *             cds exons are used
  *
--- a/src/dynlibsrc/genomicregion.pod
+++ b/src/dynlibsrc/genomicregion.pod
@@ -133,7 +133,7 @@
 
 &Wise2::GenomicRegion::write_Diana_FT_GenomicRegion(gr,ofp)
 
-  Writes Embl feature table for diana use. Does assumme that
+  Writes Embl feature table for diana use. Does assume that
   there is only one transcript per gene and only
   cds exons are used
 
@@ -152,7 +152,7 @@
 
 &Wise2::GenomicRegion::write_Embl_FT_GenomicRegion(gr,ofp)
 
-  Writes Embl feature table. Does assumme that
+  Writes Embl feature table. Does assume that
   there is only one transcript per gene and only
   cds exons are used
 
--- a/src/dynlibsrc/genomicregion.tex
+++ b/src/dynlibsrc/genomicregion.tex
@@ -164,7 +164,7 @@
 \item[ofp] [UNKN ] Undocumented argument [FILE *]
 \item[returns] Nothing - no return value
 \end{description}
-Writes Embl feature table for diana use. Does assumme that
+Writes Embl feature table for diana use. Does assume that
 there is only one transcript per gene and only
 cds exons are used
 
@@ -192,7 +192,7 @@
 \item[ofp] [UNKN ] Undocumented argument [FILE *]
 \item[returns] Nothing - no return value
 \end{description}
-Writes Embl feature table. Does assumme that
+Writes Embl feature table. Does assume that
 there is only one transcript per gene and only
 cds exons are used
 
--- a/src/dynlibsrc/genomicregion_api.h
+++ b/src/dynlibsrc/genomicregion_api.h
@@ -106,7 +106,7 @@
 
 /* Function:  Wise2_write_Diana_FT_GenomicRegion(gr,ofp)
  *
- * Descrip:    Writes Embl feature table for diana use. Does assumme that
+ * Descrip:    Writes Embl feature table for diana use. Does assume that
  *             there is only one transcript per gene and only
  *             cds exons are used
  *
@@ -125,7 +125,7 @@
 
 /* Function:  Wise2_write_Embl_FT_GenomicRegion(gr,ofp)
  *
- * Descrip:    Writes Embl feature table. Does assumme that
+ * Descrip:    Writes Embl feature table. Does assume that
  *             there is only one transcript per gene and only
  *             cds exons are used
  *
--- a/src/dynlibsrc/proteinstreamedindex.c
+++ b/src/dynlibsrc/proteinstreamedindex.c
@@ -299,7 +299,7 @@
 	}
 	add_lookup_GenericIndexResult_from_Pos(p->prev[i],psir,backtrace,waylength);
       }
-      /* can assumme this is ok */
+      /* can assume this is ok */
 
       break;
     } else {
--- a/src/dynlibsrc/proteinstreamedindex.dy
+++ b/src/dynlibsrc/proteinstreamedindex.dy
@@ -256,7 +256,7 @@
 	}
 	add_lookup_GenericIndexResult_from_Pos(p->prev[i],psir,backtrace,waylength);
       }
-      /* can assumme this is ok */
+      /* can assume this is ok */
 
       break;
     } else {
--- a/src/models/threestatemodel.c
+++ b/src/models/threestatemodel.c
@@ -470,7 +470,7 @@
  *
  * Arg:        pro [READ ] protein sequence [Protein *]
  * Arg:        mat [READ ] comparison matrix to use [CompMat *]
- * Arg:         rm [READ ] random model which you assumme the matrix was built with [RandomModel *]
+ * Arg:         rm [READ ] random model which you assume the matrix was built with [RandomModel *]
  * Arg:        gap [READ ] gap open penalty [int]
  * Arg:        ext [READ ] gap ext penalty [int]
  *
@@ -595,7 +595,7 @@
  *
  * Arg:        pro [READ ] protein sequence [Protein *]
  * Arg:        mat [READ ] comparison matrix to use [CompMat *]
- * Arg:         rm [READ ] random model which you assumme the matrix was built with [RandomModel *]
+ * Arg:         rm [READ ] random model which you assume the matrix was built with [RandomModel *]
  * Arg:        gap [READ ] gap open penalty [int]
  * Arg:        ext [READ ] gap ext penalty [int]
  *
--- a/src/models/threestatemodel.dy
+++ b/src/models/threestatemodel.dy
@@ -480,14 +480,14 @@
 
 %func 
 Makes a local three-state-model from a sequence.  this is scary
-hackery, assumming that the matrix is half-bits and normalising in a
+hackery, assuming that the matrix is half-bits and normalising in a
 *very* wrong way to get "probabilities" out.
 
 Works though
 %arg
 pro r protein sequence
 mat r comparison matrix to use
-rm  r random model which you assumme the matrix was built with
+rm  r random model which you assume the matrix was built with
 gap r gap open penalty
 ext r gap ext penalty
 %%
@@ -587,7 +587,7 @@
 
 %func
 Makes a global three-state-model from a sequence.
-Like the local version, this is scary hackery, assumming
+Like the local version, this is scary hackery, assuming
 that the matrix is half-bits and normalising in a *very*
 wrong way to get "probabilities" out.
 
@@ -595,7 +595,7 @@
 %arg
 pro r protein sequence
 mat r comparison matrix to use
-rm  r random model which you assumme the matrix was built with
+rm  r random model which you assume the matrix was built with
 gap r gap open penalty
 ext r gap ext penalty
 %%
--- a/src/models/threestatemodel.h
+++ b/src/models/threestatemodel.h
@@ -340,7 +340,7 @@
 /* Function:  ThreeStateModel_from_half_bit_Sequence(pro,mat,rm,gap,ext)
  *
  * Descrip:    Makes a local three-state-model from a sequence.  this is scary
- *             hackery, assumming that the matrix is half-bits and normalising in a
+ *             hackery, assuming that the matrix is half-bits and normalising in a
  *             *very* wrong way to get "probabilities" out.
  *
  *             Works though
@@ -348,7 +348,7 @@
  *
  * Arg:        pro [READ ] protein sequence [Protein *]
  * Arg:        mat [READ ] comparison matrix to use [CompMat *]
- * Arg:         rm [READ ] random model which you assumme the matrix was built with [RandomModel *]
+ * Arg:         rm [READ ] random model which you assume the matrix was built with [RandomModel *]
  * Arg:        gap [READ ] gap open penalty [int]
  * Arg:        ext [READ ] gap ext penalty [int]
  *
@@ -362,7 +362,7 @@
 /* Function:  global_ThreeStateModel_from_half_bit_Sequence(pro,mat,rm,gap,ext)
  *
  * Descrip:    Makes a global three-state-model from a sequence.
- *             Like the local version, this is scary hackery, assumming
+ *             Like the local version, this is scary hackery, assuming
  *             that the matrix is half-bits and normalising in a *very*
  *             wrong way to get "probabilities" out.
  *
@@ -371,7 +371,7 @@
  *
  * Arg:        pro [READ ] protein sequence [Protein *]
  * Arg:        mat [READ ] comparison matrix to use [CompMat *]
- * Arg:         rm [READ ] random model which you assumme the matrix was built with [RandomModel *]
+ * Arg:         rm [READ ] random model which you assume the matrix was built with [RandomModel *]
  * Arg:        gap [READ ] gap open penalty [int]
  * Arg:        ext [READ ] gap ext penalty [int]
  *
--- a/src/models/threestatemodel.pod
+++ b/src/models/threestatemodel.pod
@@ -95,7 +95,7 @@
 &Wise2::ThreeStateModel::ThreeStateModel_from_half_bit_Sequence(pro,mat,rm,gap,ext)
 
   Makes a local three-state-model from a sequence.  this is scary
-  hackery, assumming that the matrix is half-bits and normalising in a
+  hackery, assuming that the matrix is half-bits and normalising in a
   *very* wrong way to get "probabilities" out.
 
   Works though
@@ -104,7 +104,7 @@
 
   Argument pro          [READ ] protein sequence [Protein *]
   Argument mat          [READ ] comparison matrix to use [CompMat *]
-  Argument rm           [READ ] random model which you assumme the matrix was built with [RandomModel *]
+  Argument rm           [READ ] random model which you assume the matrix was built with [RandomModel *]
   Argument gap          [READ ] gap open penalty [int]
   Argument ext          [READ ] gap ext penalty [int]
   Return [UNKN ] Undocumented return value [ThreeStateModel *]
--- a/src/models/threestatemodel.tex
+++ b/src/models/threestatemodel.tex
@@ -126,13 +126,13 @@
 \begin{description}
 \item[pro] [READ ] protein sequence [Protein *]
 \item[mat] [READ ] comparison matrix to use [CompMat *]
-\item[rm] [READ ] random model which you assumme the matrix was built with [RandomModel *]
+\item[rm] [READ ] random model which you assume the matrix was built with [RandomModel *]
 \item[gap] [READ ] gap open penalty [int]
 \item[ext] [READ ] gap ext penalty [int]
 \item[returns] [UNKN ] Undocumented return value [ThreeStateModel *]
 \end{description}
 Makes a local three-state-model from a sequence.  this is scary
-hackery, assumming that the matrix is half-bits and normalising in a
+hackery, assuming that the matrix is half-bits and normalising in a
 *very* wrong way to get "probabilities" out.
 
 
--- a/src/models/threestatemodel_api.h
+++ b/src/models/threestatemodel_api.h
@@ -82,7 +82,7 @@
 /* Function:  Wise2_ThreeStateModel_from_half_bit_Sequence(pro,mat,rm,gap,ext)
  *
  * Descrip:    Makes a local three-state-model from a sequence.  this is scary
- *             hackery, assumming that the matrix is half-bits and normalising in a
+ *             hackery, assuming that the matrix is half-bits and normalising in a
  *             *very* wrong way to get "probabilities" out.
  *
  *             Works though
@@ -90,7 +90,7 @@
  *
  * Arg:        pro          protein sequence [Wise2_Protein *]
  * Arg:        mat          comparison matrix to use [Wise2_CompMat *]
- * Arg:        rm           random model which you assumme the matrix was built with [Wise2_RandomModel *]
+ * Arg:        rm           random model which you assume the matrix was built with [Wise2_RandomModel *]
  * Arg:        gap          gap open penalty [int]
  * Arg:        ext          gap ext penalty [int]
  *
--- a/src/dyc/type.c
+++ b/src/dyc/type.c
@@ -259,7 +259,7 @@
       if( su == NULL ) {
 	pe |= PERR_OUT_OF_SCOPE;
 	if( dycw == NULL || dycw->warn_extern == TRUE )
-	  warn("Name [%s] is out of scope: assumming extern",ExprTree->word);
+	  warn("Name [%s] is out of scope: assuming extern",ExprTree->word);
       } else {
 	/*	fprintf(stderr,"Ok.[%d] for name %s, going to add %s\n",ExprTree->attrib,ExprTree->word,su->app);*/
 	strcat(buffer,su->app);
--- a/src/dyc/type.dy
+++ b/src/dyc/type.dy
@@ -271,7 +271,7 @@
       if( su == NULL ) {
 	pe |= PERR_OUT_OF_SCOPE;
 	if( dycw == NULL || dycw->warn_extern == TRUE )
-	  warn("Name [%s] is out of scope: assumming extern",ExprTree->word);
+	  warn("Name [%s] is out of scope: assuming extern",ExprTree->word);
       } else {
 	/*	fprintf(stderr,"Ok.[%d] for name %s, going to add %s\n",ExprTree->attrib,ExprTree->word,su->app);*/
 	strcat(buffer,su->app);
--- a/src/dynlibsrc/cdna.c
+++ b/src/dynlibsrc/cdna.c
@@ -29,7 +29,7 @@
 
 /* Function:  read_fasta_file_cDNA(filename)
  *
- * Descrip:    Reads a fasta file assumming that it is cDNA. 
+ * Descrip:    Reads a fasta file assuming that it is cDNA. 
  *             Will complain if it is not, and return NULL.
  *
  *
@@ -54,7 +54,7 @@
 
 /* Function:  read_fasta_cDNA(ifp)
  *
- * Descrip:    Reads a fasta file assumming that it is cDNA. 
+ * Descrip:    Reads a fasta file assuming that it is cDNA. 
  *             Will complain if it is not, and return NULL.
  *
  *
--- a/src/dynlibsrc/cdna.dy
+++ b/src/dynlibsrc/cdna.dy
@@ -48,7 +48,7 @@
 }
 
 %func
-Reads a fasta file assumming that it is cDNA. 
+Reads a fasta file assuming that it is cDNA. 
 Will complain if it is not, and return NULL.
 %arg
 filename filename to be opened and read
@@ -67,7 +67,7 @@
 
 
 %func
-Reads a fasta file assumming that it is cDNA. 
+Reads a fasta file assuming that it is cDNA. 
 Will complain if it is not, and return NULL.
 %arg
 ifp file point to be read from
--- a/src/dynlibsrc/cdna.h
+++ b/src/dynlibsrc/cdna.h
@@ -53,7 +53,7 @@
 
 /* Function:  read_fasta_file_cDNA(filename)
  *
- * Descrip:    Reads a fasta file assumming that it is cDNA. 
+ * Descrip:    Reads a fasta file assuming that it is cDNA. 
  *             Will complain if it is not, and return NULL.
  *
  *
@@ -68,7 +68,7 @@
 
 /* Function:  read_fasta_cDNA(ifp)
  *
- * Descrip:    Reads a fasta file assumming that it is cDNA. 
+ * Descrip:    Reads a fasta file assuming that it is cDNA. 
  *             Will complain if it is not, and return NULL.
  *
  *
--- a/src/dynlibsrc/cdna.pod
+++ b/src/dynlibsrc/cdna.pod
@@ -55,7 +55,7 @@
 
 &Wise2::cDNA::read_fasta_file_cDNA(filename)
 
-  Reads a fasta file assumming that it is cDNA. 
+  Reads a fasta file assuming that it is cDNA. 
   Will complain if it is not, and return NULL.
 
 
--- a/src/dynlibsrc/cdna.tex
+++ b/src/dynlibsrc/cdna.tex
@@ -57,7 +57,7 @@
 \item[filename] [UNKN ] filename to be opened and read [char *]
 \item[returns] [UNKN ] Undocumented return value [cDNA *]
 \end{description}
-Reads a fasta file assumming that it is cDNA. 
+Reads a fasta file assuming that it is cDNA. 
 Will complain if it is not, and return NULL.
 
 
--- a/src/dynlibsrc/cdna_api.h
+++ b/src/dynlibsrc/cdna_api.h
@@ -37,7 +37,7 @@
 
 /* Function:  Wise2_read_fasta_file_cDNA(filename)
  *
- * Descrip:    Reads a fasta file assumming that it is cDNA. 
+ * Descrip:    Reads a fasta file assuming that it is cDNA. 
  *             Will complain if it is not, and return NULL.
  *
  *
--- a/src/dynlibsrc/dna.c
+++ b/src/dynlibsrc/dna.c
@@ -29,7 +29,7 @@
 
 /* Function:  read_fasta_file_DNA (filename)
  *
- * Descrip:    Reads a fasta file assumming that it is DNA. 
+ * Descrip:    Reads a fasta file assuming that it is DNA. 
  *             Will complain if it is not, and return NULL.
  *
  *
@@ -54,7 +54,7 @@
 
 /* Function:  read_fasta_DNA (ifp)
  *
- * Descrip:    Reads a fasta file assumming that it is DNA. 
+ * Descrip:    Reads a fasta file assuming that it is DNA. 
  *             Will complain if it is not, and return NULL.
  *
  *
--- a/src/dynlibsrc/dna.dy
+++ b/src/dynlibsrc/dna.dy
@@ -33,7 +33,7 @@
 }
 
 %func
-Reads a fasta file assumming that it is DNA. 
+Reads a fasta file assuming that it is DNA. 
 Will complain if it is not, and return NULL.
 %arg
 filename filename to be opened and read
@@ -52,7 +52,7 @@
 
 
 %func
-Reads a fasta file assumming that it is DNA. 
+Reads a fasta file assuming that it is DNA. 
 Will complain if it is not, and return NULL.
 %arg
 ifp file point to be read from
--- a/src/dynlibsrc/dna.h
+++ b/src/dynlibsrc/dna.h
@@ -53,7 +53,7 @@
 
 /* Function:  read_fasta_file_DNA (filename)
  *
- * Descrip:    Reads a fasta file assumming that it is DNA. 
+ * Descrip:    Reads a fasta file assuming that it is DNA. 
  *             Will complain if it is not, and return NULL.
  *
  *
@@ -68,7 +68,7 @@
 
 /* Function:  read_fasta_DNA (ifp)
  *
- * Descrip:    Reads a fasta file assumming that it is DNA. 
+ * Descrip:    Reads a fasta file assuming that it is DNA. 
  *             Will complain if it is not, and return NULL.
  *
  *
--- a/src/dynlibsrc/dynlibcross.c
+++ b/src/dynlibsrc/dynlibcross.c
@@ -31,7 +31,7 @@
 /* Function:  std_bits_Hscore(cut_off_level,report_stagger)
  *
  * Descrip:    This gives you a standard Hscore 
- *             module with a cutoff in bits (assumming
+ *             module with a cutoff in bits (assuming
  *             the score is being made from a standard
  *             Probability2Score type function).
  *
--- a/src/dynlibsrc/dynlibcross.dy
+++ b/src/dynlibsrc/dynlibcross.dy
@@ -31,7 +31,7 @@
 
 %func
 This gives you a standard Hscore 
-module with a cutoff in bits (assumming
+module with a cutoff in bits (assuming
 the score is being made from a standard
 Probability2Score type function).
 %%
--- a/src/dynlibsrc/dynlibcross.h
+++ b/src/dynlibsrc/dynlibcross.h
@@ -32,7 +32,7 @@
 /* Function:  std_bits_Hscore(cut_off_level,report_stagger)
  *
  * Descrip:    This gives you a standard Hscore 
- *             module with a cutoff in bits (assumming
+ *             module with a cutoff in bits (assuming
  *             the score is being made from a standard
  *             Probability2Score type function).
  *
--- a/src/dynlibsrc/pairbase.c
+++ b/src/dynlibsrc/pairbase.c
@@ -219,7 +219,7 @@
 
 /* Function:  make_flat_PairBaseCodonModel(cp,nonm,gap,ct)
  *
- * Descrip:    Makes a PairBaseCodonModel from a protein matrix - assumming a flat 
+ * Descrip:    Makes a PairBaseCodonModel from a protein matrix - assuming a flat 
  *             mapping to CodonMatrix
  *
  *
--- a/src/dynlibsrc/pairbase.dy
+++ b/src/dynlibsrc/pairbase.dy
@@ -210,7 +210,7 @@
 
 
 %func
-Makes a PairBaseCodonModel from a protein matrix - assumming a flat 
+Makes a PairBaseCodonModel from a protein matrix - assuming a flat 
 mapping to CodonMatrix
 %%
 PairBaseCodonModel * make_flat_PairBaseCodonModel(CompProb * cp,Probability nonm,Probability gap,CodonTable * ct)
--- a/src/dynlibsrc/pairbase.h
+++ b/src/dynlibsrc/pairbase.h
@@ -164,7 +164,7 @@
 
 /* Function:  make_flat_PairBaseCodonModel(cp,nonm,gap,ct)
  *
- * Descrip:    Makes a PairBaseCodonModel from a protein matrix - assumming a flat 
+ * Descrip:    Makes a PairBaseCodonModel from a protein matrix - assuming a flat 
  *             mapping to CodonMatrix
  *
  *
--- a/src/dynlibsrc/protein.c
+++ b/src/dynlibsrc/protein.c
@@ -29,7 +29,7 @@
 
 /* Function:  read_fasta_file_Protein (filename)
  *
- * Descrip:    Reads a fasta file assumming that it is protein. 
+ * Descrip:    Reads a fasta file assuming that it is protein. 
  *             Will complain if it is not, and return NULL.
  *
  *
@@ -57,7 +57,7 @@
 
 /* Function:  read_fasta_Protein (ifp)
  *
- * Descrip:    Reads a fasta file assumming that it is protein. 
+ * Descrip:    Reads a fasta file assuming that it is protein. 
  *             Will complain if it is not, and return NULL.
  *
  *
--- a/src/dynlibsrc/protein.dy
+++ b/src/dynlibsrc/protein.dy
@@ -48,7 +48,7 @@
 }
 
 %func
-Reads a fasta file assumming that it is protein. 
+Reads a fasta file assuming that it is protein. 
 Will complain if it is not, and return NULL.
 %arg
 filename filename to be opened and read
@@ -70,7 +70,7 @@
 
 
 %func
-Reads a fasta file assumming that it is protein. 
+Reads a fasta file assuming that it is protein. 
 Will complain if it is not, and return NULL.
 %arg
 ifp file point to be read from
--- a/src/dynlibsrc/protein.h
+++ b/src/dynlibsrc/protein.h
@@ -63,7 +63,7 @@
 
 /* Function:  read_fasta_file_Protein (filename)
  *
- * Descrip:    Reads a fasta file assumming that it is protein. 
+ * Descrip:    Reads a fasta file assuming that it is protein. 
  *             Will complain if it is not, and return NULL.
  *
  *
@@ -78,7 +78,7 @@
 
 /* Function:  read_fasta_Protein (ifp)
  *
- * Descrip:    Reads a fasta file assumming that it is protein. 
+ * Descrip:    Reads a fasta file assuming that it is protein. 
  *             Will complain if it is not, and return NULL.
  *
  *
--- a/src/models/genewisemodel.h
+++ b/src/models/genewisemodel.h
@@ -332,7 +332,7 @@
 /* Function:  GeneWise_fold_in_synchronised_RandomModel(gw,rm,cm,*ct,stop_codon_background)
  *
  * Descrip:    This function places 'log-odd' scores of the
- *             genewise model assumming that the random model
+ *             genewise model assuming that the random model
  *             is a protein model with the codon mapper system
  *             added in, *and* that the path of the random model
  *             is synchronous with the query model.
--- a/src/models/genewisemodeldb.c
+++ b/src/models/genewisemodeldb.c
@@ -233,7 +233,7 @@
 /* Function:  new_GeneWiseDB_cdna(syn,tdb,cp,cm,rmd,use_syn,flat_insert,allN)
  *
  * Descrip:    makes a new GeneWiseDB from its component parts,
- *             assumming a cDNA db.
+ *             assuming a cDNA db.
  *
  *             All the objects are hard-linked internally, so you can, if you
  *             wish, free them once passing them into this function
--- a/src/models/genewisemodeldb.dy
+++ b/src/models/genewisemodeldb.dy
@@ -220,7 +220,7 @@
 
 %func
 makes a new GeneWiseDB from its component parts,
-assumming a cDNA db.
+assuming a cDNA db.
 
 All the objects are hard-linked internally, so you can, if you
 wish, free them once passing them into this function
--- a/src/models/genewisemodeldb.h
+++ b/src/models/genewisemodeldb.h
@@ -126,7 +126,7 @@
 /* Function:  new_GeneWiseDB_cdna(syn,tdb,cp,cm,rmd,use_syn,flat_insert,allN)
  *
  * Descrip:    makes a new GeneWiseDB from its component parts,
- *             assumming a cDNA db.
+ *             assuming a cDNA db.
  *
  *             All the objects are hard-linked internally, so you can, if you
  *             wish, free them once passing them into this function
--- a/src/perl/scripts/halfwise.pl
+++ b/src/perl/scripts/halfwise.pl
@@ -141,7 +141,7 @@
 =item HMMer2.1.1
 
 type './configure' followed by 'make' in the hmmer-2.1.1 directory and then 'make install'
-(assumming you want to install in /usr/local/bin)
+(assuming you want to install in /usr/local/bin)
 
 =item bioperl-0.04.2