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.
| Option | Parameter | Description | Default Behavior |
|---|---|---|---|
| Input/Output | |||
| -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. |