File Format Converters

FaBox tools Create MrBayes input file from fasta (fasta2mrbayes); Fasta alignment joiner; etc… Alignment Format Converter FASTA to PHYLIP, etc, based on ReadSeq but handles quite a few more formats.

If I may toot our own horn here, I think that our seqmagick tool built on Biopython is pretty nice. It does all manner of things with a very simple command line interface.

Also in the autotoot spirit, DendroPy: NEWICK, NEXUS (of various variants), FASTA, PHYLIP (of various variants), NeXML.

I have been using seqmagick a lot, and I really like this tool - it is userfriendly, fast, and offers a lot of possibilities to change/modify and play with sequences, names, format, alignments, etc. Thanks to the Matsen group!

To convert single alignments using a GUI, when you have a specific program (rather than format) in mind (because unfortunately there are multiple “mutations” in the formats accepted by different programa), try ALTER