v2.0.0

Added

• phyling download list now will also print out the markersets that have already been downloaded.

• The filter module that calculate the treeness/RCV scores through PhyKIT to filter the uninformative markers. Use
  -n/--top_n_toverr to specify the number of markers you which to use in the final tree building.

• RAxML-NG and IQTree are now available for final tree building.

Removed

• Output option in download module. Now all the BUSCO datasets will be saved in the config folder ~/.phyling/HMM.

• Remove --from_checkpoint feature. Output to the previous output folder will trigger the check and automatically determine the
  rerun status.

• Remove tree building methods UPGMA and Neighbor Joining.

Changed

• Change the align module -m/--markerset behavior. It firstly searches against the given path and the config folder
  ~/.phyling/HMM if the path doesn't exist. Users can also directly specify the markerset name that has already been downloaded
  and saved in the config folder.

• Use timestamp for default output folder in align and tree module.

• Use FastTree to replace the UPGMA for the default tree building method.

Fixed

• Fix the multiprocessing issue.

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.