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paiof Public
paiof (& hamtree) - programs to compute aai + genes shared neighbor joining tree from OrthoFinder results
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bioconda-recipes Public
Forked from bioconda/bioconda-recipesConda recipes for the bioconda channel.
Shell MIT License UpdatedSep 27, 2025 -
antismash Public
Forked from antismash/antismashantiSMASH
Python GNU Affero General Public License v3.0 UpdatedSep 19, 2025 -
skDER Public
skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.
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peptides.py Public
Forked from althonos/peptides.pyPhysicochemical properties, indices and descriptors for amino-acid sequences.
Python GNU General Public License v3.0 UpdatedSep 2, 2025 -
gzip-up Public
Program to help making parallelization of bioinformatics-focused compression tasks simpler
Python Other UpdatedAug 15, 2025 -
psaps Public
Phylogenetically standardized assessment of pangenome fluidity / size
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Benchmarking targeted gene cluster detection by various bioinformatic tools.
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gravis Public
Forked from robert-haas/gravisInteractive graph visualizations with Python and HTML/CSS/JS.
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gtdb_gca_to_taxa_mappings Public
Directory with GTDB GCA accession to taxonomy mappings used by various programs.
Creative Commons Attribution 4.0 International UpdatedApr 18, 2025 -
zol Public
Forked from Kalan-Lab/zolPython BSD 3-Clause "New" or "Revised" License UpdatedDec 3, 2024 -
codoff Public
Forked from Kalan-Lab/codoffcodoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, phage, etc.) relative to the full genome.
Python BSD 3-Clause "New" or "Revised" License UpdatedJul 31, 2024 -
lsaBGC Public
Forked from Kalan-Lab/lsaBGClsaBGC - Lineage Specific Analysis of Biosynthetic Gene Clusters
Python BSD 3-Clause "New" or "Revised" License UpdatedMay 1, 2024 -
ConSequences Public
Forked from broadinstitute/ConSequencesSuite to delineate contiguous and conserved sequences from assemblies and search for their presence in raw sequencing data.
Python BSD 3-Clause "New" or "Revised" License UpdatedJul 13, 2023 -
OrthoFinder Public
Forked from davidemms/OrthoFinderPhylogenetic orthology inference for comparative genomics
Python GNU General Public License v3.0 UpdatedJun 1, 2023 -
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minima Public
Forked from jekyll/minimaMinima is a one-size-fits-all Jekyll theme for writers.
SCSS MIT License UpdatedDec 29, 2020 -
seQuoia Public
Forked from broadinstitute/seQuoiaA framework for diverse omics workflows, primarily focused on QC, processing and analysis of bacterial genomic sequencing sets.
Python GNU General Public License v3.0 UpdatedDec 22, 2020 -
ISfinder-sequences Public
Forked from thanhleviet/ISfinder-sequencesInsertion sequences (Insertion Element) [https://en.wikipedia.org/wiki/Insertion_sequence] collected from ISfinder (https://isfinder.biotoul.fr/)
UpdatedOct 6, 2020 -
Rotation-in-Anantharaman-Lab Public
Programs developed for rotation in the Anantharaman lab, includes MetaDownSampler.py - which takes in a metagenome assembly and a BAM file containing self/reflexive alignment of reads to the assemb…
Python MIT License UpdatedSep 30, 2020 -
PerMutation Public
Forked from broadinstitute/PerMutationCode and programs developed for Tn-Seq analysis of E. faecalis MMH594.
Python BSD 3-Clause "New" or "Revised" License UpdatedSep 14, 2020 -
genomes-MAGs-database Public
Forked from elizabethmcd/genomes-MAGs-databaseCreation of a database of Genbank genomes including isolate reference genomes and MAGs, and parallelizing 1000s of genome searches for a specific marker
Python UpdatedApr 28, 2020 -
Admixture Public
Forked from jacahill/AdmixtureC++ GNU General Public License v3.0 UpdatedFeb 13, 2020
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