v1.3.15

• Add missing -p meta for usage of prodigal-gv

v1.3.12

• Introduce apos (assess plasmid-ome similarity) and atpoc (assess temperate phage-ome conservation) to assess conservation of a focal sample's plasmids and phages across some set of target/database genomes (e.g. all other genomes in the same species/genus as the sample)
• Add prodigal-gv option in prepTG and fai.
• Add simple BLASTp search option in place of fai for abon.

What's Changed

• Update README.md by @raufs in #52
• Update atpoc by @raufs in #53

Full Changelog: v1.3.11...v1.3.12

v1.3.11

• Introduce abon!
• Update links to newer versions of precompiled prepTG databases for select bacterial taxa.
• Update wiki documentation.

What's Changed

• Update test_docker.sh by @raufs in #50
• Update abon by @raufs in #51

Full Changelog: v1.3.10...v1.3.11

v1.3.10

• Introduce clean up option in fai.
• Reorganize fai's results directory.
• Generate Tiny AAI figure and an XLSX spreadsheet in fai to allow for manual curation of homologous gene clusters detected.

What's Changed

• Update README.md by @raufs in #48
• Update run_tests.sh by @raufs in #49

Full Changelog: v1.3.9...v1.3.10

v1.3.9

• Correct new logic for more robustly determining consensus order introduced recently in v1.3.7.

What's Changed

• Update README.md by @raufs in #46
• Correct if/else logic when determining consensus order by @raufs in #47

Full Changelog: v1.3.8...v1.3.9

v1.3.8

• Update script for downloading annotation databases to account for changes in naming structure in the tar.gz directory with PGAP HMMs

v1.3.7

Major updates in v1.3.7

• Add option to prepTG to download premade databases for certain bacterial taxa/genera hosted on Zenodo.
• Add option to prepTG to construct a species tree based on skani ANI + neighbor-joining on Zenodo.
• Add option to provide species tree in fai and generate a phylo-heatmap of gene cluster searching results.
• Loosen restrictions around the need for a core ortholog group in zol analysis.

What's Changed

• Update README.md by @raufs in #28
• Update README.md by @raufs in #29
• Update splitDiamondResultsForFai.cpp by @raufs in #30
• Update README.md by @raufs in #31
• Update README.md by @raufs in #32
• Update CITATION.cff by @raufs in #33
• Update CITATION.cff by @raufs in #34
• update to v1.3.7 by @raufs in #35
• Update README.md by @raufs in #36
• Update README.md by @raufs in #37
• Update fai.py by @raufs in #38
• Update fai.py by @raufs in #39
• Update fai.py by @raufs in #40

Full Changelog: v1.3.6...v1.3.7

v1.3.6

• Fix conditional statement in determination of 'consensus directionality' in zol - should be flipped.

What's Changed

• Update README.md by @raufs in #26
• update to v1.3.6 by @raufs in #27

Full Changelog: v1.3.5...v1.3.6

v1.3.5

• Fix mis-spelling of "Oomolog Group" to "Ortholog Group".

What's Changed

• update to v1.3.5 by @raufs in #25

Full Changelog: v1.3.4...v1.3.5

v1.3.4

• Fix mismapping of parameter names and arguments in file for provenane for fai (introduced in 1.3.3 after incorporation of single query mode).
• Add consideration point for dereplication in zol help and README to only be used when working with gene-clusters >10kb.

What's Changed

• Update to 1.3.4 by @raufs in #24

Full Changelog: v.1.3.3...v1.3.4