pal2nal.pl1

Usage

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:

-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.