Provided by: pal2nal_14.1-3_all 
NAME
pal2nal.pl - use insight from protein alignment for nucleotide alignment
SYNOPSIS
pal2nal.pl pep.aln nuc.fasta [nuc.fasta...] [options]
DESCRIPTION
pal2nal.pl (v13)
pep.aln:
protein alignment either in CLUSTAL or FASTA format
nuc.fasta:
DNA sequences (single multi-fasta or separated files)
Options:
-h Show help
-output (clustal|paml|fasta|codon)
Output format; default = clustal
-blockonly
Show only user specified blocks '#' under CLUSTAL alignment (see example)
-nogap remove columns with gaps and inframe stop codons
-nomismatch
remove mismatched codons (mismatch between pep and cDNA) from the output
-codontable (universal|vmitochondria)
Codon table
- universal (default) - vmitochondria -> vertebrate mitochondrial
-html HTML output (only for the web server)
-nostderr
No STDERR messages (only for the web server)
- sequence order in pep.aln and nuc.fasta should be the same.
- IDs in pep.aln are used in the output.
pal2nal.pl (v13)
Usage: pal2nal.pl pep.aln nuc.fasta [nuc.fasta...] [options]
pep.aln:
protein alignment either in CLUSTAL or FASTA format
nuc.fasta:
DNA sequences (single multi-fasta or separated files)
Options:
-h Show help
-output (clustal|paml|fasta|codon)
Output format; default = clustal
-blockonly
Show only user specified blocks '#' under CLUSTAL alignment (see example)
-nogap remove columns with gaps and inframe stop codons
-nomismatch
remove mismatched codons (mismatch between pep and cDNA) from the output
-codontable (universal|vmitochondria)
Codon table
- universal (default) - vmitochondria -> vertebrate mitochondrial
-html HTML output (only for the web server)
-nostderr
No STDERR messages (only for the web server)
- sequence order in pep.aln and nuc.fasta should be the same.
- IDs in pep.aln are used in the output.
SEE ALSO
The full documentation for pal2nal.pl is maintained as a Texinfo manual. If the info and
pal2nal.pl programs are properly installed at your site, the command
info pal2nal.pl
should give you access to the complete manual.