clustalw2fasta

Usage:

clustalw2fasta [options] <alignment file>

Description

This program converts a multiple alignment in clustalw format into a FASTA file.

Input

Alignment File

A file containing one or more aligned sequences in Clustalw format.

Output

Writes FASTA formatted sequences to standard output.

The program outputs each of the sequences in the multiple alignment.

Options

Option Parameter Description Default Behaviour
Input/Output
-consensusthreshold Rather than printing each of the sequences to the FASTA file, the program prints their consensus, with gaps (hyphens) inserted whenever the consensus character occurs in less than threshold% of the sequences. Output the sequences as normal.
-nogap Do not include gap characters in the output. Include the gap characters.
-seqorderseqorder filename Output the sequences in the order given in the seqorder filename file. This file must contain a superset of the sequences in the Clustalw alignment file. Output the sequences in the same order that they appear in the input.