v1.1

Features

• VCF import now supports indels. See the documentation for details and caveats.
• MAF alignments can now be imported. See the documentation for details and caveats.
• Concatenated MFA (multi-fasta), in which all LCBs are joined, can now be output. Note that this will create spuriously contiguous sequences at LCB boundaries and should be used with caution.
• Tree branch lengths can be adjusted (with -u) to account for trees generated on only variant columns, rather than entire multi-alignments (Gingr v1.1.1 is needed to display the adjusted lengths).

Bug fixes

• Non-wrapped Fasta files (with each full sequence on one line) no longer cause hangs when importing as references.
• XMFA output when the final LCB contains no variants will no longer crash or produce infinite output.

Changes

• The binary has been renamed from harvest to harvesttools.