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'\" t
.\" Title: EMMA
.\" Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
.\" Date: 05/11/2012
.\" Manual: EMBOSS Manual for Debian
.\" Source: EMBOSS 6.4.0
.\" Language: English
.\"
.TH "EMMA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
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.\" http://bugs.debian.org/507673
.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.ie \n(.g .ds Aq \(aq
.el .ds Aq '
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.\" disable hyphenation
.nh
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.\" * MAIN CONTENT STARTS HERE *
.\" -----------------------------------------------------------------
.SH "NAME"
emma \- Multiple sequence alignment (ClustalW wrapper)
.SH "SYNOPSIS"
.HP \w'\fBemma\fR\ 'u
\fBemma\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-onlydend\ \fR\fB\fItoggle\fR\fR] \fB\-dend\ \fR\fB\fItoggle\fR\fR \fB\-dendfile\ \fR\fB\fIinfile\fR\fR [\fB\-slow\ \fR\fB\fItoggle\fR\fR] \fB\-pwmatrix\ \fR\fB\fIlist\fR\fR \fB\-pwdnamatrix\ \fR\fB\fIlist\fR\fR \fB\-usermatrix\ \fR\fB\fIvariable\fR\fR \fB\-pairwisedatafile\ \fR\fB\fIinfile\fR\fR \fB\-matrix\ \fR\fB\fIlist\fR\fR \fB\-usermamatrix\ \fR\fB\fIvariable\fR\fR \fB\-dnamatrix\ \fR\fB\fIlist\fR\fR \fB\-umamatrix\ \fR\fB\fIvariable\fR\fR \fB\-mamatrixfile\ \fR\fB\fIinfile\fR\fR \fB\-pwgapopen\ \fR\fB\fIfloat\fR\fR \fB\-pwgapextend\ \fR\fB\fIfloat\fR\fR \fB\-ktup\ \fR\fB\fIinteger\fR\fR \fB\-gapw\ \fR\fB\fIinteger\fR\fR \fB\-topdiags\ \fR\fB\fIinteger\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-nopercent\ \fR\fB\fIboolean\fR\fR [\fB\-gapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-gapextend\ \fR\fB\fIfloat\fR\fR] [\fB\-endgaps\ \fR\fB\fIboolean\fR\fR] [\fB\-gapdist\ \fR\fB\fIinteger\fR\fR] \fB\-norgap\ \fR\fB\fIboolean\fR\fR \fB\-hgapres\ \fR\fB\fIstring\fR\fR \fB\-nohgap\ \fR\fB\fIboolean\fR\fR [\fB\-maxdiv\ \fR\fB\fIinteger\fR\fR] \fB\-outseq\ \fR\fB\fIseqoutset\fR\fR \fB\-dendoutfile\ \fR\fB\fIoutfile\fR\fR
.HP \w'\fBemma\fR\ 'u
\fBemma\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBemma\fR
is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Multiple" command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
\fB\-sequence\fR \fIseqall\fR
.RS 4
.RE
.PP
\fB\-onlydend\fR \fItoggle\fR
.RS 4
Default value: N
.RE
.PP
\fB\-dend\fR \fItoggle\fR
.RS 4
Default value: N
.RE
.PP
\fB\-dendfile\fR \fIinfile\fR
.RS 4
.RE
.PP
\fB\-slow\fR \fItoggle\fR
.RS 4
A distance is calculated between every pair of sequences and these are used to construct the dendrogram which guides the final multiple alignment\&. The scores are calculated from separate pairwise alignments\&. These can be calculated using 2 methods: dynamic programming (slow but accurate) or by the method of Wilbur and Lipman (extremely fast but approximate)\&. The slow\-accurate method is fine for short sequences but will be VERY SLOW for many (e\&.g\&. >100) long (e\&.g\&. >1000 residue) sequences\&. Default value: Y
.RE
.SS "Pairwise align options"
.PP
\fB\-pwmatrix\fR \fIlist\fR
.RS 4
The scoring table which describes the similarity of each amino acid to each other\&. There are three \*(Aqin\-built\*(Aq series of weight matrices offered\&. Each consists of several matrices which work differently at different evolutionary distances\&. To see the exact details, read the documentation\&. Crudely, we store several matrices in memory, spanning the full range of amino acid distance (from almost identical sequences to highly divergent ones)\&. For very similar sequences, it is best to use a strict weight matrix which only gives a high score to identities and the most favoured conservative substitutions\&. For more divergent sequences, it is appropriate to use \*(Aqsofter\*(Aq matrices which give a high score to many other frequent substitutions\&. 1) BLOSUM (Henikoff)\&. These matrices appear to be the best available for carrying out data base similarity (homology searches)\&. The matrices used are: Blosum80, 62, 45 and 30\&. 2) PAM (Dayhoff)\&. These have been extremely widely used since the late \*(Aq70s\&. We use the PAM 120, 160, 250 and 350 matrices\&. 3) GONNET \&. These matrices were derived using almost the same procedure as the Dayhoff one (above) but are much more up to date and are based on a far larger data set\&. They appear to be more sensitive than the Dayhoff series\&. We use the GONNET 40, 80, 120, 160, 250 and 350 matrices\&. We also supply an identity matrix which gives a score of 1\&.0 to two identical amino acids and a score of zero otherwise\&. This matrix is not very useful\&. Default value: b
.RE
.PP
\fB\-pwdnamatrix\fR \fIlist\fR
.RS 4
The scoring table which describes the scores assigned to matches and mismatches (including IUB ambiguity codes)\&. Default value: i
.RE
.PP
\fB\-usermatrix\fR \fIvariable\fR
.RS 4
.RE
.PP
\fB\-pairwisedatafile\fR \fIinfile\fR
.RS 4
.RE
.SS "Matrix options"
.PP
\fB\-matrix\fR \fIlist\fR
.RS 4
This gives a menu where you are offered a choice of weight matrices\&. The default for proteins is the PAM series derived by Gonnet and colleagues\&. Note, a series is used! The actual matrix that is used depends on how similar the sequences to be aligned at this alignment step are\&. Different matrices work differently at each evolutionary distance\&. There are three \*(Aqin\-built\*(Aq series of weight matrices offered\&. Each consists of several matrices which work differently at different evolutionary distances\&. To see the exact details, read the documentation\&. Crudely, we store several matrices in memory, spanning the full range of amino acid distance (from almost identical sequences to highly divergent ones)\&. For very similar sequences, it is best to use a strict weight matrix which only gives a high score to identities and the most favoured conservative substitutions\&. For more divergent sequences, it is appropriate to use \*(Aqsofter\*(Aq matrices which give a high score to many other frequent substitutions\&. 1) BLOSUM (Henikoff)\&. These matrices appear to be the best available for carrying out data base similarity (homology searches)\&. The matrices used are: Blosum80, 62, 45 and 30\&. 2) PAM (Dayhoff)\&. These have been extremely widely used since the late \*(Aq70s\&. We use the PAM 120, 160, 250 and 350 matrices\&. 3) GONNET \&. These matrices were derived using almost the same procedure as the Dayhoff one (above) but are much more up to date and are based on a far larger data set\&. They appear to be more sensitive than the Dayhoff series\&. We use the GONNET 40, 80, 120, 160, 250 and 350 matrices\&. We also supply an identity matrix which gives a score of 1\&.0 to two identical amino acids and a score of zero otherwise\&. This matrix is not very useful\&. Alternatively, you can read in your own (just one matrix, not a series)\&. Default value: b
.RE
.PP
\fB\-usermamatrix\fR \fIvariable\fR
.RS 4
.RE
.PP
\fB\-dnamatrix\fR \fIlist\fR
.RS 4
This gives a menu where a single matrix (not a series) can be selected\&. Default value: i
.RE
.PP
\fB\-umamatrix\fR \fIvariable\fR
.RS 4
.RE
.PP
\fB\-mamatrixfile\fR \fIinfile\fR
.RS 4
.RE
.SS "Additional section"
.SS "Slow align options"
.PP
\fB\-pwgapopen\fR \fIfloat\fR
.RS 4
The penalty for opening a gap in the pairwise alignments\&. Default value: 10\&.0
.RE
.PP
\fB\-pwgapextend\fR \fIfloat\fR
.RS 4
The penalty for extending a gap by 1 residue in the pairwise alignments\&. Default value: 0\&.1
.RE
.SS "Fast align options"
.PP
\fB\-ktup\fR \fIinteger\fR
.RS 4
This is the size of exactly matching fragment that is used\&. INCREASE for speed (max= 2 for proteins; 4 for DNA), DECREASE for sensitivity\&. For longer sequences (e\&.g\&. >1000 residues) you may need to increase the default\&. Default value: @($(acdprotein)?1:2)
.RE
.PP
\fB\-gapw\fR \fIinteger\fR
.RS 4
This is a penalty for each gap in the fast alignments\&. It has little affect on the speed or sensitivity except for extreme values\&. Default value: @($(acdprotein)?3:5)
.RE
.PP
\fB\-topdiags\fR \fIinteger\fR
.RS 4
The number of k\-tuple matches on each diagonal (in an imaginary dot\-matrix plot) is calculated\&. Only the best ones (with most matches) are used in the alignment\&. This parameter specifies how many\&. Decrease for speed; increase for sensitivity\&. Default value: @($(acdprotein)?5:4)
.RE
.PP
\fB\-window\fR \fIinteger\fR
.RS 4
This is the number of diagonals around each of the \*(Aqbest\*(Aq diagonals that will be used\&. Decrease for speed; increase for sensitivity\&. Default value: @($(acdprotein)?5:4)
.RE
.PP
\fB\-nopercent\fR \fIboolean\fR
.RS 4
Default value: N
.RE
.SS "Gap options"
.PP
\fB\-gapopen\fR \fIfloat\fR
.RS 4
The penalty for opening a gap in the alignment\&. Increasing the gap opening penalty will make gaps less frequent\&. Default value: 10\&.0
.RE
.PP
\fB\-gapextend\fR \fIfloat\fR
.RS 4
The penalty for extending a gap by 1 residue\&. Increasing the gap extension penalty will make gaps shorter\&. Terminal gaps are not penalised\&. Default value: 5\&.0
.RE
.PP
\fB\-endgaps\fR \fIboolean\fR
.RS 4
End gap separation: treats end gaps just like internal gaps for the purposes of avoiding gaps that are too close (set by \*(Aqgap separation distance\*(Aq)\&. If you turn this off, end gaps will be ignored for this purpose\&. This is useful when you wish to align fragments where the end gaps are not biologically meaningful\&. Default value: Y
.RE
.PP
\fB\-gapdist\fR \fIinteger\fR
.RS 4
Gap separation distance: tries to decrease the chances of gaps being too close to each other\&. Gaps that are less than this distance apart are penalised more than other gaps\&. This does not prevent close gaps; it makes them less frequent, promoting a block\-like appearance of the alignment\&. Default value: 8
.RE
.PP
\fB\-norgap\fR \fIboolean\fR
.RS 4
Residue specific penalties: amino acid specific gap penalties that reduce or increase the gap opening penalties at each position in the alignment or sequence\&. As an example, positions that are rich in glycine are more likely to have an adjacent gap than positions that are rich in valine\&. Default value: N
.RE
.PP
\fB\-hgapres\fR \fIstring\fR
.RS 4
This is a set of the residues \*(Aqconsidered\*(Aq to be hydrophilic\&. It is used when introducing Hydrophilic gap penalties\&. Default value: GPSNDQEKR
.RE
.PP
\fB\-nohgap\fR \fIboolean\fR
.RS 4
Hydrophilic gap penalties: used to increase the chances of a gap within a run (5 or more residues) of hydrophilic amino acids; these are likely to be loop or random coil regions where gaps are more common\&. The residues that are \*(Aqconsidered\*(Aq to be hydrophilic are set by \*(Aq\-hgapres\*(Aq\&. Default value: N
.RE
.PP
\fB\-maxdiv\fR \fIinteger\fR
.RS 4
This switch, delays the alignment of the most distantly related sequences until after the most closely related sequences have been aligned\&. The setting shows the percent identity level required to delay the addition of a sequence; sequences that are less identical than this level to any other sequences will be aligned later\&. Default value: 30
.RE
.SS "Output section"
.PP
\fB\-outseq\fR \fIseqoutset\fR
.RS 4
.RE
.PP
\fB\-dendoutfile\fR \fIoutfile\fR
.RS 4
.RE
.SH "BUGS"
.PP
Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
.SH "SEE ALSO"
.PP
emma is fully documented via the
\fBtfm\fR(1)
system\&.
.SH "AUTHOR"
.PP
\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
.SH "COPYRIGHT"
.br
.PP
This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
.sp
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