Having the proper data file format is essential as many programs can only input certain file types. The following are some of the input and output file formats for specific programs.

CLUSTAL file format:
Programs that input this file type: Clustal W/X
Programs that output this file type: Clustal W/X

FASTA file format:
Programs that input this file type: Clustal W/X, MAFFT
Programs that output this file type: Clustal W/X, MAFFT

NEXUS file format:
Programs that input this file type: BEAUti, GARLI, Modeltest, MrBayes, PAUP*
Programs that output this file type: Clustal W/X, PAUP*

PHYLIP file format:
Programs that input this file type: GARLI, LAMARC, Migrate-n, PAML, PHYLIP
Programs that output this file type: Clustal W/X, PAUP*, PHYLIP

PIR file format:
Programs that input this file type: Clustal W/X
Programs that output this file type: Clustal W/X

 

File Conversion Programs
ALTER is a useful service for converting between various multiple sequence alignment (MSA) formats.
DataConvert 1.0 can convert CLUSTAL, FASTA, MEGA, NEXUS, and PHYLIP data file types for both Macintosh and Windows platforms.
ReadSeq can convert all of the above data file types.
PGDSpider can convert many data formats common in population genetics and phylogenetics