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PAL2NAL.PL(1) User Commands PAL2NAL.PL(1)

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)

protein alignment either in CLUSTAL or FASTA format
DNA sequences (single multi-fasta or separated files)
-h Show help
-output (clustal|paml|fasta|codon)
Output format; default = clustal
Show only user specified blocks '#' under CLUSTAL alignment (see example)
remove columns with gaps and inframe stop codons
remove mismatched codons (mismatch between pep and cDNA) from the output
-codontable (universal|vmitochondria)
Codon table
- universal (default) - vmitochondria -> vertebrate mitochondrial
HTML output (only for the web server)
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]

protein alignment either in CLUSTAL or FASTA format
DNA sequences (single multi-fasta or separated files)
-h Show help
-output (clustal|paml|fasta|codon)
Output format; default = clustal
Show only user specified blocks '#' under CLUSTAL alignment (see example)
remove columns with gaps and inframe stop codons
remove mismatched codons (mismatch between pep and cDNA) from the output
-codontable (universal|vmitochondria)
Codon table
- universal (default) - vmitochondria -> vertebrate mitochondrial
HTML output (only for the web server)
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.

November 2010 pal2nal.pl