v2.0.0-beta

Changed

• Use ClipKIT to replace the self-defined function for trimming off the sites that display poor phylogenetic signal.
• Move the MSA concatenate function from align module to tree module. Users who want to try different tree building strategy won't have to rerun the align module again.
• Replace the VeryFastTree with FastTree for stability.

Added

• Check for duplicated sample names.
• Report problematic cds sequences.
• Use checkpoint file to save the hmmsearch results to prevent rerunning the search process when adding/removing samples.

Fixed

• Fix the bug caused by translation from cds sequences with invalid length.
• Fix the bug caused by inconsistent MSA output extension.
• Fix the bug that the trimming function always return peptide MSA if the sequence has no site being trimmed.
• Fix the Python logger issue.

v0.9.0

Fix workflows

v1.1beta Intermediate release

Archive of current code for citation and release, but there are revisions still in progress. Included a CITATION.cff file and some of the framework for BUSCO marker set use direct from unannotated genomes.