JLSteenwyk
Omics & Software Eng 🧬👨🏽💻 | HHMI Awardee of the LSRF & Berkeley Science Fellow at UC-Berkeley 🐻👨🏽🔬 | Previous HHMI Gilliam Fellow at Vanderbilt🧬🎓
University of California, BerkeleyBerkeley, CA
Pinned Repositories
BioKIT
a versatile toolkit for processing and analyzing diverse types of sequence data
ClipKIT
a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
ggpubfigs
colorblind friendly color palettes and ggplot2 graphic system extensions for publication-quality scientific figures
latch_library
A library of code snippets used in Latch SDK development
Molecular_sequence_analyses_scripts
orthofisher
a broadly applicable tool for automated gene identification and retrieval
orthosnap
a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
PhyKIT
a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
Phylogenetic_scripts
treehouse
A shiny R application to prune phylogenies in our database or user input and obtain a subtree
JLSteenwyk's Repositories
JLSteenwyk/ggpubfigs
colorblind friendly color palettes and ggplot2 graphic system extensions for publication-quality scientific figures
JLSteenwyk/ClipKIT
a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
JLSteenwyk/PhyKIT
a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
JLSteenwyk/orthofisher
a broadly applicable tool for automated gene identification and retrieval
JLSteenwyk/orthosnap
a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
JLSteenwyk/BioKIT
a versatile toolkit for processing and analyzing diverse types of sequence data
JLSteenwyk/latch_library
A library of code snippets used in Latch SDK development
JLSteenwyk/treehouse
A shiny R application to prune phylogenies in our database or user input and obtain a subtree
JLSteenwyk/Phylogenetic_scripts
JLSteenwyk/Molecular_sequence_analyses_scripts
JLSteenwyk/fun_scripts
a repository of fun scripts I have written
JLSteenwyk/Awesome-LatchBio
A curated list of awesome Bioinformatics pipelines and software available on LatchBio
JLSteenwyk/budding_yeast_coevolution_network
Budding yeast coevolution network
JLSteenwyk/jlsteenwyk.github.io
JLSteenwyk/my_latch_workflows
repository of all the LatchBio workflows I've written
JLSteenwyk/mycotools
JLSteenwyk/Pathogenic_allodiploid_hybrids_of_Aspergillus_fungi
Holds code and files associated with Pathogenic allodiploid hybrids of Aspergillus fungi
JLSteenwyk/2024_phylogenomics_workshop
2024 workshop on phylogenomics, organized by Evomics
JLSteenwyk/api-test
simple case of how to build an API
JLSteenwyk/cookiecutter-data-science
A logical, reasonably standardized, but flexible project structure for doing and sharing data science work.
JLSteenwyk/goatools
Python scripts to find enrichment of GO terms
JLSteenwyk/integRATE
integRATE
JLSteenwyk/latch
A toolchain to define serverless bioinformatics workflows with plain python and deploy no-code interfaces with a single command.
JLSteenwyk/latch_wf_clipkit
workflow for launching ClipKIT on the Latch platform
JLSteenwyk/latch_wf_codon_optimization
JLSteenwyk/latch_wf_infer_phylogeny
JLSteenwyk/latch_wf_orthosnap
OrthoSNAP workflow for LatchBio SDK
JLSteenwyk/latch_wf_seq_to_tree
codebase for latch workflow that infers the evolutionary history for a set of sequences
JLSteenwyk/noveltree
NovelTree is a highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionary history.
JLSteenwyk/PHYling
Unified 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)