clustalw2fasta [options] <alignment file>
This program converts a multiple alignment in clustalw format into a FASTA 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.
|-consensus||threshold||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.|
|-seqorder||seqorder 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.|