orthologs

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.

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

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).

A pipeline to reconstruct a species tree with RaxML, from Single-Copy Orthologues (SCOs) identified by OrthoFinder.

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 unified bioinformatics tool for exploring evolutionarily conserved 🧬 proteins across model organisms. Combines multi-database ortholog search with Gene Ontology annotation extension. 🎓 PhD project, King's College London (2013-2019).

Mapping RefSeq RNA to OrthoDB (Under Development)

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