Phylogenetic orthology inference for comparative genomics
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Updated
Mar 30, 2024 - Python
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
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
Find reciprocal best hits (DIAMOND or BLAST) between two (or more!) sets of sequences.
scripts to process, join, split, or add new proteins to a supermatrix alignment using hmms
Feature-aware Directed OrtholoG search
🍣 🦐 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
Mapping RefSeq RNA to OrthoDB (Under Development)
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)
Supplementay Material for publication "Species-specific molecular responses of wild coral reef fishes during a marine heatwave"
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