Scripts used to help facilitate the construction of a binary protein interaction network
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Updated
Mar 14, 2018 - Python
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"
Script to design core genome phylogeny using bacterial genome assemblies
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.
Ortholog/homolog mapping for Geneweaver
Mapping RefSeq RNA to OrthoDB (Under Development)
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).
GUI tool to add rich annotations to PAW summary files from Swiss-Prot flat text files.
ortho2align is a lncRNA ortholog discovery CLI tool based on syntenic regions and statistical assessment of alignment nonrandomness.
🍣 🦐 A lightweight nucleotide bacterial ortholog clustering tool
Feature-aware Directed OrtholoG search
scripts to process, join, split, or add new proteins to a supermatrix alignment using hmms
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.
Assembly of Phylogenomic Datasets from High-Throughput Sequencing data
A high performance tool to identify orthologs and paralogs across genomes.
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