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University of California, Berkeley
- Berkeley, CA
- jlsteenwyk.com
- @JLSteenwyk
- https://genomely.substack.com
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ClipKIT Public
a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
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PhyKIT Public
a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
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orthofisher Public
a broadly applicable tool for automated gene identification and retrieval
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BioKIT Public
a versatile toolkit for processing and analyzing diverse types of sequence data
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orthosnap Public
a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
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2024_phylogenomics_workshop Public
2024 workshop on phylogenomics, organized by Evomics
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ggpubfigs Public
colorblind friendly color palettes and ggplot2 graphic system extensions for publication-quality scientific figures
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mycotools Public
Forked from xonq/mycotools -
noveltree Public
Forked from Arcadia-Science/noveltreeNovelTree is a highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionary history.
Nextflow GNU Affero General Public License v3.0 UpdatedOct 9, 2023 -
PHYling Public
Forked from stajichlab/PHYlingUnified PHYling pipeline for species tree building from annotated genomes (see https://github.com/stajichlab/AAFTF and https://github.com/nextgenusfs/funannotate for assembly and annotation steps)
Python MIT License UpdatedOct 5, 2023 -
latch_library Public
A library of code snippets used in Latch SDK development
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my_latch_workflows Public
repository of all the LatchBio workflows I've written
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latch Public
Forked from latchbio/latchA toolchain to define serverless bioinformatics workflows with plain python and deploy no-code interfaces with a single command.
Python UpdatedJun 16, 2022 -
latch_wf_seq_to_tree Public
codebase for latch workflow that infers the evolutionary history for a set of sequences
Python UpdatedJun 16, 2022 -
Awesome-LatchBio Public
Forked from nahid18/Awesome-LatchBioA curated list of awesome Bioinformatics pipelines and software available on LatchBio
1 UpdatedMay 21, 2022 -
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latch_wf_clipkit Public
workflow for launching ClipKIT on the Latch platform
Python UpdatedMay 11, 2022 -
treehouse Public
A shiny R application to prune phylogenies in our database or user input and obtain a subtree
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Budding yeast coevolution network
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Holds code and files associated with Pathogenic allodiploid hybrids of Aspergillus fungi
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goatools Public
Forked from tanghaibao/goatoolsPython scripts to find enrichment of GO terms
Python BSD 2-Clause "Simplified" License UpdatedSep 26, 2017 -
cookiecutter-data-science Public
Forked from drivendataorg/cookiecutter-data-scienceA logical, reasonably standardized, but flexible project structure for doing and sharing data science work.
Python MIT License UpdatedJul 21, 2017