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2024_phylogenomics_workshop

2024 workshop on phylogenomics, organized by Evomics

api-test

simple case of how to build an API

awesome-latchbio

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

biokit

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

budding_yeast_coevolution_network

Budding yeast coevolution network

clipkit

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

cookiecutter-data-science

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

fun_scripts

a repository of fun scripts I have written

ggpubfigs

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

goatools

Python scripts to find enrichment of GO terms

hybridcheck

HybridCheck, an R package for quickly scripting scans of sequence data for recombination regions.

integrate

integRATE

jlsteenwyk.github.io

latch

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

latch_library

A library of code snippets used in Latch SDK development

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

molecular_sequence_analyses_scripts

my_latch_workflows

repository of all the LatchBio workflows I've written

mycotools

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.

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

pathogenic_allodiploid_hybrids_of_aspergillus_fungi

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

phykit

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

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)

phylogenetic_scripts