clustalw2fasta [options] <alignment file>


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


<alignment file>

The name of a file containing one or more aligned sequences in Clustalw format.


Writes FASTA formatted sequences to standard output.

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


Option Parameter Description Default Behavior
-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.