Repositories list

• Phyling

  Public
  Phyling: phylogenetic inference from annotated genomes

  pythonphylogeneticssoftware+ 3

  pythonphylogeneticssoftwarehidden-markov-modelphylogenomicsorthology

  Python

  •

  MIT License

  •55 forks•3333 stars•33 issues•99 pull requests•Updated Apr 13, 2026Apr 13, 2026

• adhesionPred

  Public
  Adhesion protein prediction

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•33 pull requests•Updated Apr 11, 2026Apr 11, 2026

• Antarctica_Endolithic_Eukaryotic_MAG

  Public
  Eukaryotic MAGs from Endolithic metagenome sampling

  Shell

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026

• stajichlab.github.io

  Public
  Stajich Lab Website

  genomefungimycology

  genomefungimycology

  HTML

  •

  BSD 3-Clause "New" or "Revised" License

  •435435 forks•00 stars•00 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026

• orthoSynAssign

  Public
  Assign orthologs within many-many groups with synteny

  Python

  •

  GNU General Public License v3.0

  •00 forks•22 stars•00 issues•00 pull requests•Updated Apr 7, 2026Apr 7, 2026

• PopGenomics_Afumigatus_Global

  Public
  A. fumigatus population genomics 2021 relaunch

  HTML

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 6, 2026Apr 6, 2026

• Caulerpa_genomes

  Public
  Genome sequencing of Caulerpa genomes

  AMPL

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 26, 2026Mar 26, 2026

• Antrim_Shale_Fungal_Genomes

  Public
  Antrim Shale genomes from Quinn Moon cultures

  Shell

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 24, 2026Mar 24, 2026

• biosample_metadata

  Public
  Extract metadata from biosamples in NCBI

  bioinformaticsncbi-srancbi-biosamples+ 1

  bioinformaticsncbi-srancbi-biosamplesbiosample

  Python

  •

  MIT License

  •11 fork•1717 stars•11 issue•00 pull requests•Updated Mar 12, 2026Mar 12, 2026

• AAFTF

  Public
  Automatic Assembly For The Fungi

  Python

  •

  MIT License

  •66 forks•2626 stars•1717 issues•00 pull requests•Updated Mar 11, 2026Mar 11, 2026

• Fungi_5k

  Public
  Fungi5k dataset analysis

  Python

  •11 fork•11 star•00 issues•00 pull requests•Updated Feb 28, 2026Feb 28, 2026

• DhingraLab_Afum_ncRNA_temperature

  Public
  A. fumigatus Temp and delta-ncRNA analysis

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 17, 2026Feb 17, 2026

• Afumigatus_RefStrains

  Public
  Reference A. fumigatus strain panel

  Shell

  •00 forks•11 star•00 issues•00 pull requests•Updated Feb 13, 2026Feb 13, 2026

• PopGenomics_Coccidioides_2025

  Public
  Combined analysis set for 2025 freeze of Coccidioides strains

  Shell

  •11 fork•11 star•00 issues•00 pull requests•Updated Feb 6, 2026Feb 6, 2026

• DhingraLab_Afum_AzoleAdapted

  Public
  Azole Adapted Afumigatus strain resequencing

  HTML

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 23, 2026Jan 23, 2026

• Massospora_RNAseq

  Public
  Some exploring expression from cicada plugs (2024 samples)

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 22, 2026Jan 22, 2026

• KassonLab_Mycangium_RNAseq

  Public
  Mycangium RNAseq

  HTML

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 15, 2026Jan 15, 2026

• PopGenomics_template

  Public template
  Template for Population Genomics variant calling

  Shell

  •

  MIT License

  •22 forks•33 stars•22 issues•00 pull requests•Updated Jan 7, 2026Jan 7, 2026

• CramerLab_Afumigatus_AF293_VOR

  Public
  Explore AF293 VOR Strain Evolution

  HTML

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Dec 18, 2025Dec 18, 2025

• DhingraLab_ncRNA_Afumigatus

  Public
  Afumigatus ncRNA discovery from RNASeq and comparative approach

  R

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 21, 2025Nov 21, 2025

• RelocaTE3

  Public
  ReLocaTE code for identifying Transposons (TE) in genomes using re-sequencing data

  Python

  •

  MIT License

  •11 fork•33 stars•44 issues•00 pull requests•Updated Nov 19, 2025Nov 19, 2025

• Acarospora_socialis_pangenome

  Public
  Pangenome from A. socialis CCGP and herbarium resequencing project

  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 12, 2025Nov 12, 2025

• ExtremeRhodotorula_RefGenomes

  Public
  Reference Genome Assembly and Annotation for Rhodotorula genomes in "Extreme Rhodotorula" project

  Shell

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 2, 2025Jul 2, 2025

• Afumigatus_pangenome

  Public
  A. fumigatus pangenome analyses

  Pep8

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 17, 2025Jun 17, 2025

• RolshausenLab_Aspergillus_DatePalm

  Public
  Aspergillus tubingensis DFA genome sequencing and annotation

  Shell

  •

  MIT License

  •11 fork•11 star•00 issues•00 pull requests•Updated Jun 15, 2025Jun 15, 2025

• ExtremeRhodotorula_Hybrid_Diploid

  Public
  Investigating potential diploid/hybrid strains

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 13, 2025Jun 13, 2025

• Annotation_Aspergillus_melleus

  Public
  Annotation of the previously published A. melleus CBS 546.65 genome

  Shell

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 18, 2025May 18, 2025

• DhingraLab_Azole_RNASeq

  Public
  Azole exposure RNASeq across 2 Afumigatus genotypes

  R

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 2, 2025May 2, 2025

• PopGenomics_Cimmitis

  Public
  Population Genomics and CNV analysis of C. immitis strains

  HTML

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 23, 2025Apr 23, 2025

• PopGenomics_Cposadasii

  Public
  C.posa variant calling and CNV exploration using

  Shell

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 23, 2025Apr 23, 2025