Jacob L. Steenwyk

ggpubfigs. colorblind friendly color palettes and ggplot2 graphic system extensions for publication-quality scientific figures

ClipKIT. a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

PhyKIT. a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies

orthofisher. a broadly applicable tool for automated gene identification and retrieval

orthohmm. Improved Inference of Ortholog Groups using Hidden Markov Models

orthosnap. a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

BioKIT. a versatile toolkit for processing and analyzing diverse types of sequence data

treehouse. A shiny R application to prune phylogenies in our database or user input and obtain a subtree

latch_library. A library of code snippets used in Latch SDK development

gokit. Command-line toolkit for Gene Ontology (GO) enrichment analysis

clustkit. accurate protein sequence clustering

Phylogenetic_scripts. Python

pypubfigs. publication-quality themes and colorblind-friendly palettes for seaborn and matplotlib

Molecular_sequence_analyses_scripts. Python

plmtogo. a small protein language model based off of nanochat

fun_scripts. a repository of fun scripts I have written

ecomp. evolutionary compression of multiple sequence alignments

budding_yeast_coevolution_network. Budding yeast coevolution network

remarkit. Ranking phylogEnomic MARKers using Information Theory and machine learning

my_latch_workflows. repository of all the LatchBio workflows I've written

Pathogenic_allodiploid_hybrids_of_Aspergillus_fungi. Holds code and files associated with Pathogenic allodiploid hybrids of Aspergillus fungi

2024_phylogenomics_workshop. 2024 workshop on phylogenomics, organized by Evomics

sm_scipresence. Python

JLSteenwyk.

cross_poster. cross post to Bluesky, Twitter, and LinkedIn

oaktree. Python

starkit. Python

Awesome-LatchBio. A curated list of awesome Bioinformatics pipelines and software available on LatchBio