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
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)
A small pipeline to extract homologs from Homologene
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.
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
Find reciprocal best hits (DIAMOND or BLAST) between two (or more!) sets of sequences.
An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵
Assembly of Phylogenomic Datasets from High-Throughput Sequencing data
A high performance tool to identify orthologs and paralogs across genomes.
Phylogenetic orthology inference for comparative genomics
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