Files must be provided in formats recognized by the individual code. Typically a tool has one or two formats that are accepted as input, and we rely on the user to provide data in the correct format. We provide support for interconversion of many file formats with the tools Readseq and NCL Converter. NCL Converter is the prefered tool for converting NEXUS files to relaxed Phylip format (as required for RAxML). READSEQ is not reliable for parsing Nexus into other formats. On the other hand, the Normalized Nexus produced by NCL Converter is not recognized by MrBayes 3.1.2, because characters and taxa are broken into separate blocks. The differences are explained on the Nexus page below. Documentation of some common formats is provided below. The text has been liberally borrowed from a variety of sources.
FASTA (fasta; multiple fasta; aligned fasta)
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CIPRES – Cyberinfrastructure for Phylogenic Research