From pairs of most similar sequences to phylogenetic best matches

Authors Peter F. Stadler
Manuela Geiß
David Schaller
Alitzel López Sánchez
Marcos González Laffitte
Dulce I. Valdivia
Marc Hellmuth
Maribel Hernández Rosales
Editors
Title From pairs of most similar sequences to phylogenetic best matches
Type article
Journal Algorithms for Molecular Biology
Volume 15
DOI 10.1186/s13015-020-00165-2
Month April
Year 2020
SCCH ID# 20024
Abstract

Many of the commonly used methods for orthology detection start from mutually most similar pairs of genes (reciprocal best hits) as an approximation for evolutionary most closely related pairs of genes (reciprocal best matches). This approximation of best matches by best hits becomes exact for ultrametric dissimilarities, i.e., under the Molecular Clock Hypothesis. It fails, however, whenever there are large lineage specific rate variations among paralogous genes. In practice, this introduces a high level of noise into the input data for best-hit-based orthology detection methods.