a3288ea
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chtsai0105
Cheng-Hung Tsai
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.