orthologs

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.

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

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

Feature-aware Directed OrtholoG search

🍣 🦐 A lightweight nucleotide bacterial ortholog clustering tool

scripts to add new proteins to alignment using hmms

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

Mapping RefSeq RNA to OrthoDB (Under Development)

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

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).

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

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

A small pipeline to extract homologs from Homologene

Submit PA locus tags and download annotations or sequences, and map to other strains

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

Script to design core genome phylogeny using bacterial genome assemblies