.\" Automatically generated by Pod::Man 4.09 (Pod::Simple 3.35)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
..
.de Vb \" Begin verbatim text
.ft CW
.nf
.ne \\$1
..
.de Ve \" End verbatim text
.ft R
.fi
..
.\" Set up some character translations and predefined strings.  \*(-- will
.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
.\" double quote, and \*(R" will give a right double quote.  \*(C+ will
.\" give a nicer C++.  Capital omega is used to do unbreakable dashes and
.\" therefore won't be available.  \*(C` and \*(C' expand to `' in nroff,
.\" nothing in troff, for use with C<>.
.tr \(*W-
.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
.ie n \{\
.    ds -- \(*W-
.    ds PI pi
.    if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
.    if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\"  diablo 12 pitch
.    ds L" ""
.    ds R" ""
.    ds C` ""
.    ds C' ""
'br\}
.el\{\
.    ds -- \|\(em\|
.    ds PI \(*p
.    ds L" ``
.    ds R" ''
.    ds C`
.    ds C'
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is >0, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.\"
.\" Avoid warning from groff about undefined register 'F'.
.de IX
..
.if !\nF .nr F 0
.if \nF>0 \{\
.    de IX
.    tm Index:\\$1\t\\n%\t"\\$2"
..
.    if !\nF==2 \{\
.        nr % 0
.        nr F 2
.    \}
.\}
.\" ========================================================================
.\"
.IX Title "PRANK 1"
.TH PRANK 1 "2018-05-27" "v.121211" "The Probabilistic Alignment Kit"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
prank \- Computes probabilistic multiple sequence alignments
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
\&\fBprank\fR \fIsequence_file\fR
.PP
\&\fBprank\fR [optional parameters] \-d=\fIsequence_file\fR [optional parameters]
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
The Probabilistic Alignment Kit (\s-1PRANK\s0) is a probabilistic multiple alignment
program for \s-1DNA,\s0 codon and amino-acid sequences. It's based on a novel algorithm
that treats insertions correctly and avoids over-estimation of the number of
deletion events.
.PP
In addition, \s-1PRANK\s0 borrows ideas from maximum likelihood methods used in
phylogenetics and correctly takes into account the evolutionary distances
between sequences. Lastly, \s-1PRANK\s0 allows for defining a potential structure for
sequences to be aligned and then, simultaneously with the alignment, predicts
the locations of structural units in the sequences.
.SH "OPTIONS"
.IX Header "OPTIONS"
.SS "\s-1INPUT/OUTPUT PARAMETERS\s0"
.IX Subsection "INPUT/OUTPUT PARAMETERS"
.IP "\fB\-d=\f(BIsequence_file\fB\fR" 8
.IX Item "-d=sequence_file"
The input sequence file in \s-1FASTA\s0 format.
.IP "\fB\-t=\f(BItree_file\fB\fR" 8
.IX Item "-t=tree_file"
The tree file to use. If unset, an appriximated \s-1NJ\s0 tree is generated.
.IP "\fB\-o=\f(BIoutput_file\fB\fR" 8
.IX Item "-o=output_file"
Set the name of the output file. If unset, \fIoutput_file\fR is set to \fBoutput\fR.
.IP "\fB\-f=\f(BIoutput_format\fB\fR" 8
.IX Item "-f=output_format"
Set the output format. \fIoutput_format\fR can be one of \fBfasta\fR (default),
\&\fBphylipi\fR, \fBphylips\fR, \fBpaml\fR, or \fBnexus\fR.
.IP "\fB\-m=\f(BImodel_file\fB\fR" 8
.IX Item "-m=model_file"
The model file to use. If unset, \fImodel_file\fR is set to \fB\s-1HKY2/WAG\s0\fR.
.IP "\fB\-support\fR" 8
.IX Item "-support"
Compute posterior support.
.IP "\fB\-showxml\fR" 8
.IX Item "-showxml"
Output alignment xml-file.
.IP "\fB\-showtree\fR" 8
.IX Item "-showtree"
Output alignment guidetree.
.IP "\fB\-showanc\fR" 8
.IX Item "-showanc"
Output ancestral sequences.
.IP "\fB\-showall\fR" 8
.IX Item "-showall"
Output all of these.
.IP "\fB\-noanchors\fR" 8
.IX Item "-noanchors"
Do not use Exonerate anchoring. (Exonerate to be installed separately.)
.IP "\fB\-nomafft\fR" 8
.IX Item "-nomafft"
Do not use \s-1MAFFT\s0 for guide tree. (\s-1MAFFT\s0 to be installed separately.)
.IP "\fB\-njtree\fR" 8
.IX Item "-njtree"
Estimate tree from an input alignment (and realign).
.IP "\fB\-shortnames\fR" 8
.IX Item "-shortnames"
Truncate names at first space character.
.IP "\fB\-quiet\fR" 8
.IX Item "-quiet"
Reduce output.
.SS "\s-1ALIGNMENT MERGE\s0"
.IX Subsection "ALIGNMENT MERGE"
.IP "\fB\-d1=\f(BIalignment_file\fB\fR" 8
.IX Item "-d1=alignment_file"
The first input alignment file in \s-1FASTA\s0 format.
.IP "\fB\-d2=\f(BIalignment_file\fB\fR" 8
.IX Item "-d2=alignment_file"
The second input alignment file in \s-1FASTA\s0 format.
.IP "\fB\-t1=\f(BItree_file\fB\fR" 8
.IX Item "-t1=tree_file"
The tree file for the first alignment. If unset, an appriximated \s-1NJ\s0 tree is generated.
.IP "\fB\-t2=\f(BItree_file\fB\fR" 8
.IX Item "-t2=tree_file"
The tree file for the second alignment. If unset, an appriximated \s-1NJ\s0 tree is generated.
.SS "\s-1MODEL PARAMETERS\s0"
.IX Subsection "MODEL PARAMETERS"
.IP "\fB\-F\fR, \fB+F\fR" 8
.IX Item "-F, +F"
Force insertions to be always skipped.
.IP "\fB\-gaprate=\f(BI#\fB\fR" 8
.IX Item "-gaprate=#"
Set the gap opening rate. The default is \fB0.025\fR for \s-1DNA\s0 and \fB0.005\fR for
proteins.
.IP "\fB\-gapext=\f(BI#\fB\fR" 8
.IX Item "-gapext=#"
Set the gap extension probability. The default is \fB0.75\fR for \s-1DNA\s0 and \fB0.5\fR for
proteins.
.IP "\fB\-codon\fR" 8
.IX Item "-codon"
Use empirical codon model for coding \s-1DNA.\s0
.IP "\fB\-DNA\fR, \fB\-protein\fR" 8
.IX Item "-DNA, -protein"
Use \s-1DNA\s0 or protein model, respectively. Disables auto-detection of model.
.IP "\fB\-termgap\fR" 8
.IX Item "-termgap"
Penalise terminal gaps normally.
.IP "\fB\-nomissing\fR" 8
.IX Item "-nomissing"
No missing data. Use \fB\-F\fR for terminal gaps.
.IP "\fB\-keep\fR" 8
.IX Item "-keep"
Do not remove gaps from pre-aligned sequences.
.SS "\s-1OTHER PARAMETERS\s0"
.IX Subsection "OTHER PARAMETERS"
.IP "\fB\-iterate=#\fR" 8
.IX Item "-iterate=#"
Rounds of re-alignment iteration; by default, iterate five times and keep the best result.
.IP "\fB\-once\fR" 8
.IX Item "-once"
Run only once. Same as \-iterate=1.
.IP "\fB\-prunetree\fR" 8
.IX Item "-prunetree"
Prune guide tree branches with no sequence data.
.IP "\fB\-prunedata\fR" 8
.IX Item "-prunedata"
Prune sequence data with no guide tree leaves.
.IP "\fB\-uselogs\fR" 8
.IX Item "-uselogs"
Slower but should work for a greater number of sequences.
.IP "\fB\-translate\fR" 8
.IX Item "-translate"
Translate input data to protein sequences.
.IP "\fB\-mttranslate\fR" 8
.IX Item "-mttranslate"
Translate input data to protein sequencess using mt table.
.IP "\fB\-convert\fR" 8
.IX Item "-convert"
Do not align, just convert to a different format.
.IP "\fB\-dna=\f(BIdna_sequence_file\fB\fR" 8
.IX Item "-dna=dna_sequence_file"
\&\s-1DNA\s0 sequence file for backtranslation of protein alignment.
.IP "\fB\-help\fR" 8
.IX Item "-help"
Show an extended help page with more options.
.IP "\fB\-version\fR" 8
.IX Item "-version"
Show version and check for updates.
.SH "AUTHORS"
.IX Header "AUTHORS"
\&\fBprank\fR was written by Ari Loytynoja.
.PP
This manual page was originally written by Manuel Prinz <manuel@debian.org> for
the Debian project (and may be used by others).