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.

pal2nal.pl                                        November 2010                                    PAL2NAL.PL(1)