JLSteenwyk

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

ggpubfigs

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

orthofisher

a broadly applicable tool for automated gene identification and retrieval

BioKIT

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

orthosnap

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

latch_library

A library of code snippets used in Latch SDK development

treehouse

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

Phylogenetic_scripts

Molecular_sequence_analyses_scripts

fun_scripts

a repository of fun scripts I have written

Awesome-LatchBio

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

budding_yeast_coevolution_network

Budding yeast coevolution network

jlsteenwyk.github.io

my_latch_workflows

repository of all the LatchBio workflows I've written

mycotools

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

api-test

simple case of how to build an API

cookiecutter-data-science

A logical, reasonably standardized, but flexible project structure for doing and sharing data science work.

goatools

Python scripts to find enrichment of GO terms

integRATE

integRATE

latch

A toolchain to define serverless bioinformatics workflows with plain python and deploy no-code interfaces with a single command.

latch_wf_clipkit

workflow for launching ClipKIT on the Latch platform

latch_wf_codon_optimization

latch_wf_infer_phylogeny

latch_wf_orthosnap

OrthoSNAP workflow for LatchBio SDK

latch_wf_seq_to_tree

codebase for latch workflow that infers the evolutionary history for a set of sequences

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.

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)