Phylogenetic orthology inference for comparative genomics

A phylogenetic profile analysis tool

An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵

A high performance tool to identify orthologs and paralogs across genomes.

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

Find reciprocal best hits (DIAMOND or BLAST) between two (or more!) sets of sequences.

CLfinder-OrthNet, a pipeline to encode orthologs from multiple genomes and their evolutionary history into networks (OrthNets) based on co-linearity between them. OrthNets enable detection of all orthologous gene groups that share the same evolutionary history, using a search based on network topology

Feature-aware Directed OrtholoG search

scripts to process, join, split, or add new proteins to a supermatrix alignment using hmms

🍣 🦐 A lightweight nucleotide bacterial ortholog clustering tool

ortho2align is a lncRNA ortholog discovery CLI tool based on syntenic regions and statistical assessment of alignment nonrandomness.

GUI tool to add rich annotations to PAW summary files from Swiss-Prot flat text files.

PhyProbe is a bioinformatic pipeline designed to extract phylogenetic loci from Next-Generation Sequencing datasets including RNAseq, WGS, and Sequence/Target Capture methodologies (e.g., AHE, UCEs).

Ortholog/homolog mapping for Geneweaver

A Compi pipeline for finding orthologs using a two-way BLAST approach.

Mapping RefSeq RNA to OrthoDB (Under Development)

R package for the statistical detection of orthogroups associated to plant traits pointing to specific genes that might be present of absence and are good candidate genes responsible for the plant trait.

Scripts used to help facilitate the construction of a binary protein interaction network

A small pipeline to extract homologs from Homologene

Archive of personal scripts repository from my various projects in the Buell Lab at MSU (Jan. 2008 - Apr. 2011)