Kalan-Lab/zol issues and pull requests

#92 - 1.5.8

Pull Request - State: closed - Opened by raufs about 2 months ago

#91 - Add options to control inflation parameter for MCL and to perform simple single-linkage clustering for ortholog group delineation.

Issue - State: closed - Opened by raufs about 2 months ago

#90 - Correct `generateSyntenicVisual.py` usage with new setup which generates R scripts (will be addressed in v1.5.6).

Issue - State: closed - Opened by raufs about 2 months ago

#89 - Add flag to avoid replacing start proteins with `M` if they are instead `L` or `V` based on direct translation (implemented with bacteria in mind) if eukaryotic analysis is being performed (will be addressed in v1.5.6).

Issue - State: closed - Opened by raufs about 2 months ago

#88 - Correct FASTA output for near-core representative proteins for fai parameter suggestions in zol and handling of cases when 0 or only 1 core proteins are found (will be addressed in v1.5.6).

Issue - State: closed - Opened by raufs about 2 months ago

#87 - update to v1.5.6

Pull Request - State: closed - Opened by raufs about 2 months ago

#86 - Regarding zol & fai usage on viral contigs

Issue - State: open - Opened by ShailNair 2 months ago - 2 comments

#85 - Update CITATION.cff

Pull Request - State: closed - Opened by raufs 3 months ago

#84 - Update util.py

Pull Request - State: closed - Opened by raufs 3 months ago

#83 - Update zol.py

Pull Request - State: closed - Opened by raufs 3 months ago

#82 - Update meta.yaml

Pull Request - State: closed - Opened by raufs 3 months ago

#81 - Update README.md

Pull Request - State: closed - Opened by raufs 3 months ago

#80 - Update README.md

Pull Request - State: closed - Opened by raufs 3 months ago

#79 - Update CITATION.cff

Pull Request - State: closed - Opened by raufs 3 months ago

#78 - Update to v1.5.0

Pull Request - State: closed - Opened by raufs 3 months ago

#77 - Update CITATION.cff

Pull Request - State: closed - Opened by raufs 6 months ago

#76 - Incorporate an option for automatic visualization options for dereplicated gene cluster instances in zol (e.g. using pygenomeviz or clinker)

Issue - State: closed - Opened by raufs 7 months ago - 1 comment

#75 - Add options for skani sketching/searching, in particular for marker k-mer compression factor.

Issue - State: closed - Opened by raufs 7 months ago - 1 comment

#74 - Update annotateProtSeqs.py

Pull Request - State: closed - Opened by raufs 7 months ago

#73 - Update README.md

Pull Request - State: closed - Opened by raufs 7 months ago

#72 - Update setup.py

Pull Request - State: closed - Opened by raufs 7 months ago

#71 - Update zol.py

Pull Request - State: closed - Opened by raufs 7 months ago

#70 - Update zol.py

Pull Request - State: closed - Opened by raufs 7 months ago

#69 - Update zol.py

Pull Request - State: closed - Opened by raufs 7 months ago

#68 - Update cgc

Pull Request - State: closed - Opened by raufs 8 months ago

#67 - Delete Efaecalis_V583_epa_proteins.faa

Pull Request - State: closed - Opened by raufs 9 months ago

#66 - Update util.py

Pull Request - State: closed - Opened by raufs 10 months ago

#65 - Update fai

Pull Request - State: closed - Opened by raufs 12 months ago

#64 - Raufs patch 3

Pull Request - State: closed - Opened by raufs about 1 year ago

#63 - Update prepTG

Pull Request - State: closed - Opened by raufs about 1 year ago

#62 - Update prepTG

Pull Request - State: closed - Opened by raufs about 1 year ago

#61 - Update README.md

Pull Request - State: closed - Opened by raufs about 1 year ago

#60 - Update/match-up default E-value cutoff in simple BLAST options for abon, apos, and atpoc

Pull Request - State: closed - Opened by raufs about 1 year ago

#59 - Update README.md

Pull Request - State: closed - Opened by raufs about 1 year ago

#58 - Update README.md

Pull Request - State: closed - Opened by raufs about 1 year ago

#57 - Update runProdigalAndMakeProperGenbank.py

Pull Request - State: closed - Opened by raufs about 1 year ago

#56 - Update setup.py

Pull Request - State: closed - Opened by raufs about 1 year ago

#55 - Update apos

Pull Request - State: closed - Opened by raufs about 1 year ago

#54 - Update ZOL

Pull Request - State: closed - Opened by raufs about 1 year ago

#53 - Update atpoc

Pull Request - State: closed - Opened by raufs about 1 year ago