| bl2seq | bl2seq sequence input/output stream |
| clustalw | clustalw sequence input/output stream |
| emboss | Parse EMBOSS alignment output (from applications water and needle) |
| fasta | FastA MSA Sequence input/output stream |
| mase | mase sequence input/output stream |
| mega | Parse and Create MEGA format data files |
| meme | meme sequence input/output stream |
| msf | msf sequence input/output stream |
| nexus | NEXUS format sequence input/output stream |
| pfam | pfam sequence input/output stream |
| phylip | PHYLIP format sequence input/output stream |
| prodom | prodom sequence input/output stream |
| psi | Read/Write PSI-BLAST profile alignment files |
| selex | selex sequence input/output stream |
| stockholm | stockholm sequence input/output stream |