A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
FastOMA is a scalable software package to infer orthology relationship.
An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵
a broadly applicable tool for automated gene identification and retrieval
a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
Workflow for identifying and classifying homologous gene/protein sequences
a python package for automated generation of phylogenetic trees from genbank files
Feature-aware orthology prediction tool. Provided data package: Quest for Orthologs reference gene sets 2019.
Feature-aware Directed OrtholoG search
Collection of scripts for gene age sorting and multi-omics data mining and analysis
Supplementary data and pipelines for analyzing genome gene content data and morphology to create various phylogenies.
This curation tool allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions.
Research compendium for Viscardi et al, 2020.
Tree-based orthology inference with functionality for reducing contamination
A stand-alone tool for evaluating simple statistics of orthologs
A Bio2BEL package for the terminology from FlyBase (http://flybase.org/)
The Docker integration for the r2g project.
A Bio2BEL package for converting Entrez and HomoloGene to BEL
A Bio2BEL package for converting the Mouse Genome Informatics Database (MGI) to BEL
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