.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.38.2.
.TH PAL2NAL.PL "1" "November 2010" "pal2nal.pl " "User Commands"
.SH NAME
pal2nal.pl \- use insight from protein alignment for nucleotide alignment
.SH SYNOPSIS
.B pal2nal.pl
\fIpep.aln  nuc.fasta  \fR[\fInuc.fasta\fR...]  [\fIoptions\fR]
.SH DESCRIPTION
pal2nal.pl  (v13)
.TP
pep.aln:
protein alignment either in CLUSTAL or FASTA format
.TP
nuc.fasta:
DNA sequences (single multi\-fasta or separated files)
.TP
Options:
\fB\-h\fR            Show help
.IP
\fB\-output\fR (clustal|paml|fasta|codon)
.IP
Output format; default = clustal
.TP
\fB\-blockonly\fR
Show only user specified blocks
\&'#' under CLUSTAL alignment (see example)
.TP
\fB\-nogap\fR
remove columns with gaps and inframe stop codons
.TP
\fB\-nomismatch\fR
remove mismatched codons (mismatch between
pep and cDNA) from the output
.IP
\fB\-codontable\fR (universal|vmitochondria)
.IP
Codon table
.IP
\- universal (default)
\- vmitochondria \-> vertebrate mitochondrial
.TP
\fB\-html\fR
HTML output (only for the web server)
.TP
\fB\-nostderr\fR
No STDERR messages (only for the web server)
.IP
\- sequence order in pep.aln and nuc.fasta should be the same.
.IP
\- IDs in pep.aln are used in the output.
.PP
pal2nal.pl  (v13)
.PP
Usage:  pal2nal.pl  pep.aln  nuc.fasta  [nuc.fasta...]  [options]
.TP
pep.aln:
protein alignment either in CLUSTAL or FASTA format
.TP
nuc.fasta:
DNA sequences (single multi\-fasta or separated files)
.TP
Options:
\fB\-h\fR            Show help
.IP
\fB\-output\fR (clustal|paml|fasta|codon)
.IP
Output format; default = clustal
.TP
\fB\-blockonly\fR
Show only user specified blocks
\&'#' under CLUSTAL alignment (see example)
.TP
\fB\-nogap\fR
remove columns with gaps and inframe stop codons
.TP
\fB\-nomismatch\fR
remove mismatched codons (mismatch between
pep and cDNA) from the output
.IP
\fB\-codontable\fR (universal|vmitochondria)
.IP
Codon table
.IP
\- universal (default)
\- vmitochondria \-> vertebrate mitochondrial
.TP
\fB\-html\fR
HTML output (only for the web server)
.TP
\fB\-nostderr\fR
No STDERR messages (only for the web server)
.IP
\- sequence order in pep.aln and nuc.fasta should be the same.
.IP
\- IDs in pep.aln are used in the output.
.SH "SEE ALSO"
The full documentation for
.B pal2nal.pl
is maintained as a Texinfo manual.  If the
.B info
and
.B pal2nal.pl
programs are properly installed at your site, the command
.IP
.B info pal2nal.pl
.PP
should give you access to the complete manual.