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<pre>
/////////////////////////////////////////////////////////////////////////////////////
// //
// INDELible V1.03 control file - settings.txt //
// //
// How to include paup blocks, set seeds for the random number generator, //
// change the output format for generated data, or how to print "reports" //
// //
/////////////////////////////////////////////////////////////////////////////////////
<font color=red>[TYPE] NUCLEOTIDE 2</font> // nucleotide simulation using algorithm from method 2
//
// * If a command is not specified in the [SETTINGS] block then it will have the
// default value shown below. The only exception to this is [randomseed] whose
// value will be randomly chosen if not specified.
// * If no [SETTINGS] block is specified all commands will have these default values.
// * More information on each of the commands can be found at the end of the file.
//
<font color=red>[SETTINGS] </font>
<font color=red>[ancestralprint]</font> FALSE // NEW, SAME or FALSE
<font color=red>[output]</font> PHYLIP // FASTA, NEXUS, PHYLIP or PHYLIPT
<font color=red>[phylipextension]</font> phy // any alpha-numeric string
<font color=red>[nexusextension]</font> nex // any alpha-numeric string
<font color=red>[fastaextension]</font> fas // any alpha-numeric string
<font color=red>[randomseed]</font> 1568746 // any integer
<font color=red>[printrates]</font> FALSE // FALSE or TRUE
<font color=red>[insertaslowercase]</font> TRUE // FALSE or TRUE
<font color=red>[markdeletedinsertions]</font> FALSE // FALSE or TRUE
<font color=red>[printcodonsasaminoacids]</font> FALSE // FALSE or TRUE
<font color=red>[fileperrep]</font> FALSE // FALSE or TRUE
<font color=red>[MODEL] mymodel [submodel] JC </font>
<font color=red>[TREE] t1 ((A:0.1,B:0.1):0.1,(C:0.1,D:0.1):0.1);</font>
<font color=red>[PARTITIONS] Pname [t1 mymodel 1000]</font> // tree t1, model mymodel, root length 1000
<font color=red>[EVOLVE] Pname 10 filename</font> // 10 replicates generated from partition Pname
/*
<font color=blue><a name="[ancestralprint]">[ancestralprint]</a></font>
* <i>NEW</i> will print ancestral sequences in a separate file to leaf sequences.
* <i>SAME</i> prints ancestral sequences in the same file as the leaf sequences.
* <i>FALSE</i> will not print any ancestral sequences.
* It should be noted that if you used different guide trees for different partitions
in a partitioned (multi-gene) analysis then only the root sequence will be printed
in the SAME/NEW file specified in this command.
<font color=blue>[output]</font>
* Unaligned sequences are always output in FASTA format as e.g. filename.fas
* This command sets the output type for the true alignment and prints it to a file
named e.g. filename_TRUE.phy
* <i>FASTA</i>, <i>NEXUS</i>, <i>PHYLIP</i> will print out sequences to file in either
fasta, nexus, or phylip format respectively.
* FASTA is used by NCBI and accepted by most sequence alignment programs.
NEXUS is used by e.g. MacClade, Mesquite, ModelTest, MrBayes and PAUP*.
PHYLIP is used by PHYLIP and PAML.
* <i>PHYLIPT</i> gives PHYLIP format with filenames truncated to 8 characters.
<font color=blue>[phylipextension]</font>
* This command sets the file extension for true alignments in phylip format so they
are e.g. filename.phy or whatever you choose them to be.
<font color=blue>[nexusextension]</font>
* This command sets the file extension for true alignments in nexus format so they
are e.g. filename.nex or whatever you choose them to be.
<font color=blue>[fastaextension]</font>
* This command sets the file extension for fasta formatted output files so they
are e.g. filename.fas or whatever you choose them to be.
<font color=blue>[randomseed]</font>
* This must be an integer value and is used to seed the random number generator.
* Running simulations with the same random seed value (and the same control file)
will produce identical datasets.
<font color=blue>[printrates]</font>
* <i>TRUE</i> will print out a detailed output file for each replicate of each block
that lists what the site-classes or relative rates of substitution are.
* <i>FALSE</i> will not print any rates information.
* Follow these links for examples of the output for <a href="nucleotide_RATES.txt" target="_blank";>NUCLEOTIDE / AMINOACID</a> simulations,
or for <a href="codon_RATES.txt" target="_blank";>CODON</a> simulations.
<font color=blue>[markdeletedinsertions]</font>
* <i>TRUE</i> will output inserted bases/residues that have been subsequently been
deleted as * rather than - for easy identification.
* <i>FALSE</i> leave everything as -.
<font color=blue>[insertaslowercase]</font>
* <i>TRUE</i> will output inserted bases/residues as lower case letters for easy identification.
* <i>FALSE</i> will output all bases/residues as upper case letters.
<font color=blue>[printcodonsasaminoacids]</font>
* <i>TRUE</i> will output codon datasets as amino-acids - how they are translated will
depend on the genetic code specified in the model.
* <i>FALSE</i> will print codons as nucleotide triplets.
<font color=blue>[fileperrep]</font>
* <i>TRUE</i> will output each replicate dataset in a separate file.
Unaligned sequences will go in e.g. filename_1.fas, filename_2.fas, etc
The true alignment will go in e.g. filename_TRUE_1.phy, filename_TRUE_2.phy, etc
* <i>FALSE</i> will print all replicates in a single file.
Unaligned sequences for each dataset will all go in e.g. filename.fas
All the true alignments will go in e.g. filename_TRUE.phy
* If a file called paupstart.txt (or paupend.txt) exists in the same directory as
INDELible then it will be copied to the beginning (or end) of each file.
* If a file called paupmiddle.txt exists in the same directory as INDELible then it
will be copied to e.g. filename_TRUE.phy after each replicate datset.
* These features are useful if you want to include PAUP or MrBayes blocks in your files.
*/
</pre>
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