v1.4.11

• correct issue with cpus argument for pyhmmer being accidentally renamed to threads in the switch of terminology from cpus to threads for zol code made in v1.4.10
• add option to skip annotations in zol, --skip-annotations
• add shebang in annotateProtaSeqs.py to make it executable.

Full Changelog: v1.4.10...v1.4.11

v1.4.10

minor updates

• update and further polish arguments (e.g. underscores to dashs).
• add --small-genomes preset flag for skani based dereplication in zol.
• (for bioconda) planning on adding constraints on versions for some dependencies (e.g. muscle>=5.0)
  Full Changelog: v1.4.9...v1.4.10

v1.4.9

• Add small script for standalone annotation using zol's standard annotation approach for consensus sequences of ortholog groups called annotateProtSeqs.py.

What's Changed

• Update README.md by @raufs in #73
• Update annotateProtSeqs.py by @raufs in #74

Full Changelog: v1.4.8...v1.4.9

v1.4.8

• re-configure where multiprocessing.set_start_method() is set in fai and add catches for possible issues to work as intended on newer Macs.
• add cgc command to tests

What's Changed

• Update setup.py by @raufs in #72

Full Changelog: v1.4.7...v1.4.8

v1.4.7

• Update usage of pomegrenate for HMM mode in fai for finding gene clusters to account for API changes.
• This is largely to update versions for some dependencies (mainly biopython and pomegrenate) in bioconda to assist in the transition to newer python versions.

v1.4.6

• add option to provide pre-computed ortholog group designations for locus tags in zol.

v1.4.5

• make inputting gene clusters to zol more flexible.
• change defaults to quicker and lower memory usage: default alignment mode is now super5 in MUSCLE and calculation of BetaRD-gc statistics are now only performed if requested via the -b argument.
• clean up more temporary files in the subdirectory for determining ortholog groups in zol.
• add note on computational resource requirements in README.

What's Changed

• Update cgc by @raufs in #68

Full Changelog: v1.4.4...v1.4.5

v1.4.4

• bump version twice to v1.4.4 - creating new release to have correct version reflected in bioconda
• deleted releases v1.4.2 and v1.4.3 from github (they are still available on Zenodo)

Major updates in v1.4.2 included:

• introduce the cgc program for large scale summary visualization of homologous gene cluster instances
• introduce the salt program for determining signatures of support for horizontal/lateral transfer following fai based identification of gene cluster instances.
• small updates throughout but no major alterations to the core functionalities.

Full Changelog: v1.4.3...v1.4.4
Full Changelog: v1.4.1...v1.4.2

v1.4.1

• revert to non-parallelized splitting of DIAMOND alignment results in findOrthologs.py.

Full Changelog: v1.4.0...v1.4.1

v1.4.0

• Correct fai cutoff for minimum proportion of distinct query genes to properly account for the occurrence of intermediate/background genes. The calculation reported in spreadsheets was not affected.
• Set default syntenic correlation threshold to 0.0 (off) from previous default of 0.6.
• Update prepTG to reference data from GTDB R220 and allow users the option to choose GTDB release (>= R214 supported).
• Update splitting of DIAMOND alignment in zol to allow for parallelization.
• Introduce CD-HIT protein clustering option/mode instead of the default InParanoid-like approach.
• Add option to control re-inflation CD-HIT parameters.
• New scripts and tutorial on using fast.genomics and CAGECAT to get sets of homologous gene clusters to investigate in zol.