Tree inference tools require an uploaded matrix of characters in a format appropriate for the target software package. The most common required formats for tree inference are: NEXUS Phylip relaxed Phylip, Aligned FASTA and CLUSTAL. Of equal importance are the XML formats used by BEAST and BEAST2, but these input files are best created using the desktop BEAUti tool provided by developers of the respective tools. The code is distributed with the individual packages, and should be downloaded for the versions of BEAST/BEAST2 you intend to use. NCLconverter and Readseq are provided to assist users in interconverting NEXUS, Phylip, and aligned FASTA formats. NCL Converter is the preferred tool for converting NEXUS files to relaxed Phylip format (as required for RAxML). READSEQ is not reliable for parsing Nexus into other formats.
Ancilllary files containing starting trees, constraints, partitions, etc. may also be required. These must also be uploaded to the data area in a format appropriate for the specific tool being used. Users should consult the manual for the code of interest for details about the proper format of any required auxilliary files.
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