pal2nal.pl - use insight from protein alignment for nucleotide
alignment
pal2nal.pl pep.aln nuc.fasta [nuc.fasta...]
[options]
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.
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.