Recent Releases of omamer
omamer - v2.0.4
What's Changed
- [FIX] freeze numpy dependency to <2 (issue #34)
- [ADD] experimental support to build omamer databases from orthoxml/fasta files
- Bump pypa/gh-action-pypi-publish from 1.8.12 to 1.9.0 by @dependabot in https://github.com/DessimozLab/omamer/pull/33
Full Changelog: https://github.com/DessimozLab/omamer/compare/v2.0.3...v2.0.4
- Python
Published by alpae over 1 year ago
omamer - v2.0.2
- changed method for hiding taxa in build process. Now takes a file containing taxa to hide on separate lines.
- checks and improved feedback for root taxon and requested taxa to hide.
- root taxon set by default to the root level in speciestree.nwk (previously hard-coded to default to LUCA)
- Python
Published by alex-wave over 2 years ago
omamer - v2.0.1
What's Changed
- remove dependency for filehash library
- return better error message if build dependencies are not met, but trying to building an omamer database
- minor fixes
- Bump actions/checkout from 3 to 4 by @dependabot in https://github.com/DessimozLab/omamer/pull/24
Full Changelog: https://github.com/DessimozLab/omamer/compare/v2.0.0...v2.0.1
- Python
Published by alpae over 2 years ago
omamer - v2.0.0
- Major update of database format and search code to improve overall memory useage. Most standard runs with LUCA-level database will run on a machine with 16GB RAM.
- Update to the scoring algorithm for root-level HOG / family assignments, to allow for significance testing. This estimates a binomial distribution for each family, so that we can compute thee probability of matching at least as many k-mers as we have observed by chance, for each family that has a match to a given query.
- UX improvements - more feedback during interactive search runs, whilst maintaining small log files.
- Python
Published by alex-wave over 2 years ago