v1.1.1

New features

• tree module now supports RAxML-NG and FastTree
• tree module now generates a RAxML-style partition file containing the positions of the core genes from the resulting MSA
• tree --no-inference mode will stop the process right before the phylogenetic inference; useful if you only need an alignment or a partition file
• createdb --custom-lookup option accepts a Foldseek database with pre-computed 3Di sequences to lookup
• profile module now gives a warning if a species contains less than 50% of the defined core genes

Bug fixes

• Fixed behavior of the --afdb-lookup option

Misc

• --afdb-local option is now deprecated and merged into the --afdb-lookup option

v1.1.0

Major update

• createdb - full support of Foldseek-ProstT5
  • Requires Foldseek version 10 or higher (detail)
  • PyTorch ProstT5 is now deprecated
• gene-tree module
  • Phylogenetic tree inference from individual core structures

Misc

• config module
  • Check and control the runtime configuration, especially regarding dependent binaries
• Improved visibility of help messages
• Minor fixes

v1.0.2

• easy-core module usability update
  • Fixed issue #1 raising error in createdb module run with Python script
• Step-by-step tutorial with example dataset
• Intermediate headers now use pseudo-random names derived from the input sequence (to aid cases such as #3)
• More user-friendly messages to track the progress and results
• Minor improvements

v1.0.1

• Quick fix on the path detection logic from Conda environment
• Added citation to the bioRxiv preprint

v1.0.0

Initial release with Conda compatibility