2.0 release

This release is associated with submission of a Software Application Note. Sample configurations are part of the release, for calculation of several pangene sets and gene families of several sizes and characteristics.

1.0 release

This is a 1.0 release. It has been used in production to generate pan-gene sets for six genera (Arachis, Cicer, Glycine, Medicago, Vigna, Phaseolus) for the PeanutBase, and SoyBase, and LegumeInfo projects.

The main change in this release relative to the previous one (2023-01-26) is the addition of the "cluster_rest" step, which clusters sequences leftover after the synteny-based clustering of the "main" annotations. This combination (synteny + clustered leftovers) is used as the basis for the homology-based addition of sequences from "extra" annotations, if provided.

Full Changelog: 2023-01-26...v2023-03-29

2023-January release candidate

Release intended for production work. Updates include: more details in the run statistics; simplified CLI requiring only the -c (config) flag; inclusion of protein files in output; updated handling of thresholds for "core" sets.

2022 end

Functional release, tested for pan-gene sets at the genus level for several legume genera and for Zea.
Handles inputs that include either "main"+"extra" annotations, or just "main" annotations.
Future releases may change the way consensus sequences are chosen and may add other output types, such as pan-gene alignments.