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Jason Stajich Lab at UC Riverside

Evolutionary Genomics of Fungi projects, data and software

35 followers
RIverside, CA
http://lab.stajich.org
@stajichlab
jason.stajich@ucr.edu

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README.md

These repositories for the Stajich laboratory at UC Riverside focused on Genomics, Bioinformatics, Evolution of (mostly) Fungi and Microbes.

https://lab.stajich.org

See our Standard Operating Procedures are (in progress) documentation on procedures and onboarding.

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Phyling Phyling Public

Phyling: phylogenetic inference from annotated genomes

Python 33 5
AAFTF AAFTF Public

Automatic Assembly For The Fungi

Python 26 6
SOP_data SOP_data Public

Standard Operating Procedures

1
funannotate_template funannotate_template Public template

Project template for doing a funannotate annotation set

Shell 3 1
PopGenomics_template PopGenomics_template Public template

Template for Population Genomics variant calling

Shell 3 2
Comparative_pipeline Comparative_pipeline Public

Comparative genomics pipeline

Perl 11 6

Repositories

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Showing 10 of 230 repositories

Fungi_BFD Public
Fungi Big-Fun-Data

stajichlab/Fungi_BFD’s past year of commit activity

Python 0 0 0 0 Updated Jun 19, 2026
RelocaTE3 Public
ReLocaTE code for identifying Transposons (TE) in genomes using re-sequencing data

stajichlab/RelocaTE3’s past year of commit activity

Python 3 MIT 0 2 0 Updated Jun 19, 2026
Phyling Public
Phyling: phylogenetic inference from annotated genomes

stajichlab/Phyling’s past year of commit activity

Python 33 MIT 5 4 7 Updated Jun 18, 2026
nf_phyling Public
Nextflow pipeline for multi-locus fungal phylogenomics: PHYling → PhyKIT → ModelTest-NG → IQ-TREE 3 → RAxML-NG

stajichlab/nf_phyling’s past year of commit activity

Nextflow 0 0 0 0 Updated Jun 18, 2026
AAFTF Public
Automatic Assembly For The Fungi

stajichlab/AAFTF’s past year of commit activity

Python 26 MIT 6 9 0 Updated Jun 16, 2026
nf_euk_genome_annotate Public
Annotation strategy for Eukaryotic genomes with auto incorporation of public evidence

stajichlab/nf_euk_genome_annotate’s past year of commit activity

Nextflow 0 0 0 0 Updated Jun 16, 2026
SSF_PRB_Fungal_Genomes Public
Powder River Basin cultured fungal genomes

stajichlab/SSF_PRB_Fungal_Genomes’s past year of commit activity

Shell 0 MIT 0 0 0 Updated Jun 16, 2026
stajichlab.github.io Public Forked from greenelab/lab-website-template
Stajich Lab Website

stajichlab/stajichlab.github.io’s past year of commit activity

HTML 0 BSD-3-Clause 443 0 0 Updated Jun 15, 2026
Cramer_Kordana_HrmA_sector Public

stajichlab/Cramer_Kordana_HrmA_sector’s past year of commit activity

HTML 0 0 0 0 Updated Jun 12, 2026
Trebouxia_Schmitt Public
Duplication analysis

stajichlab/Trebouxia_Schmitt’s past year of commit activity

Shell 0 0 0 0 Updated Jun 11, 2026

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