Jacob L. Steenwyk's Projects
2024 workshop on phylogenomics, organized by Evomics
simple case of how to build an API
A curated list of awesome Bioinformatics pipelines and software available on LatchBio
a versatile toolkit for processing and analyzing diverse types of sequence data
Budding yeast coevolution network
a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
A logical, reasonably standardized, but flexible project structure for doing and sharing data science work.
a repository of fun scripts I have written
colorblind friendly color palettes and ggplot2 graphic system extensions for publication-quality scientific figures
Python scripts to find enrichment of GO terms
HybridCheck, an R package for quickly scripting scans of sequence data for recombination regions.
integRATE
A toolchain to define serverless bioinformatics workflows with plain python and deploy no-code interfaces with a single command.
A library of code snippets used in Latch SDK development
workflow for launching ClipKIT on the Latch platform
OrthoSNAP workflow for LatchBio SDK
codebase for latch workflow that infers the evolutionary history for a set of sequences
repository of all the LatchBio workflows I've written
NovelTree is a highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionary history.
a broadly applicable tool for automated gene identification and retrieval
a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
Holds code and files associated with Pathogenic allodiploid hybrids of Aspergillus fungi
a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
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)