Data from: Integrating sequence evolution into probabilistic orthology analysis ...

• Main Authors: Ullah, Ikram, Sjöstrand, Joel, Andersson, Peter, Sennblad, Bengt, Lagergren, Jens
• Format: Dataset
• Language: English
• Published: Dryad 2015
• Subjects: Gene duplication; Mus musculus; Ciona intestinalis; Ornithorhynchus anatinus; Probabilistic Modeling; Danio rerio; Comparative genomics; Homo Sapiens; Tree Realization; gene loss; relaxed molecular clock; orthology; Tree Reconciliation; Canis lupus familiaris; Taeniopygia guttata; paralogy; Sequence Evolution; Monodelphis domestica; Gallus gallus; Canis lupus
• Online Access: https://dx.doi.org/10.5061/dryad.4r910; https://datadryad.org/stash/dataset/doi:10.5061/dryad.4r910

Orthology analysis, that is, finding out whether a pair of homologous genes are orthologs — stemming from a speciation — or paralogs — stemming from a gene duplication - is of central importance in computational biology, genome annotation, and phylogenetic inference. In particular, an orthologous relationship makes functional equivalence of the two genes highly likely. A major approach to orthology analysis is to reconcile a gene tree to the corresponding species tree, (most commonly performed using the most parsimonious reconciliation, MPR). However, most such phylogenetic orthology methods infer the gene tree without considering the constraints implied by the species tree and, perhaps even more importantly, only allow the gene sequences to influence the orthology analysis through the a priori reconstructed gene tree. We propose a sound, comprehensive Bayesian Markov chain Monte Carlo-based method, DLRSOrthology, to compute orthology probabilities. It efficiently sums over the possible gene trees and ... : Supplementary Material for “Integrating Sequence Evolution into Probabilistic Orthology Analysis”This document contains the supplementary information including synthetic data parameters, figures, and tables for the paper “Integrating Sequence Evolution into Probabilistic Orthology Analysis”Supplementary_Material.pdf ...