TY - JOUR AU - Stadler, Peter F. AU - Geiß, Manuela AU - Schaller, David AU - López Sánchez, Alitzel AU - González Laffitte, Marcos AU - Valdivia, Dulce I. AU - Hellmuth, Marc AU - Hernández Rosales, Maribel PY - 2020 DA - 2020/04/09 TI - From pairs of most similar sequences to phylogenetic best matches JO - Algorithms for Molecular Biology SP - 5 VL - 15 IS - 1 AB - 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. SN - 1748-7188 UR - https://doi.org/10.1186/s13015-020-00165-2 DO - 10.1186/s13015-020-00165-2 ID - Stadler2020 ER -