From pairs of most similar sequences to phylogenetic best matches.

ABSTRACT:

Background

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.

Results

If additive distances between genes are known, then evolutionary most closely related pairs can be identified by considering certain quartets of genes provided that in each quart

SUBMITTER: Stadler PF 

PROVIDER: S-EPMC7147060 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature