Phylogenetic orthology inference for comparative genomics

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

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.

Feature-aware Directed OrtholoG search

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

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).

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

A robust command-line and web pipeline to fetch, align, and strictly filter orthologous sequences from NCBI databases.

Mapping RefSeq RNA to OrthoDB (Under Development)

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

Orthologs Databases — Archive of bioinformatics databases and PHP processing pipelines for cross-species ortholog analysis across 7 model organisms (2012-2016). Integrates data from 21 sources including HomoloGene, InParanoid, OrthoMCL, eggNOG, BioGRID, STRING, Gene Ontology, KEGG, and Reactome.

💻 Archive of my bioinformatics tool for exploring evolutionarily conserved 🧬 proteins across five model organisms using orthology databases (eggNOG, inParanoid, Homologene etc.). 🎓 Part of my PhD project, King's College London (2013-2019).