pal2nal.pl1
Use insight from protein alignment for nucleotide alignment
Usage
pal2nal.pl pep.aln
nuc.fasta
[nuc.fasta ...]
[options]
Overview
pal2nal.pl (v13)
pep.aln:
|
protein alignment either in CLUSTAL or FASTA format |
|---|---|
nuc.fasta:
|
DNA sequences (single multi-fasta or separated files) |
Options:
|
|
|
|
|
|
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
|
|
|
|
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:
|
|
|
|
|
|
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
|
|
|
|
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. |
Releases
Unchanged in 4 releases since Debian 10 (Buster).