ArticleBriefings in bioinformatics2017
Heterogeneous molecular processes among the causes of how sequence similarity scores can fail to recapitulate phylogeny.
Article in Briefings in bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- A chromosome-level, haplotype-resolved genome assembly for the barn owl, Tyto alba.GigaScience · 2026Article
- Discovery of diverse anellovirus sequences in Thai human sequencing data.Microbiology spectrum · 2025Article
- Refined Phylogenetic Ortholog Inference Reveals Coevolutionary Expansion of the MAPK Signaling Network Through Finetuning of Pathway Specificity.Journal of molecular evolution · 2025Article
- Orphan genes are not a distinct biological entity.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- phyloBARCODER: A Web Tool for Phylogenetic Classification of Eukaryote Metabarcodes Using Custom Reference Databases.Molecular biology and evolution · 2024Article
- Major Revisions in Pancrustacean Phylogeny and Evidence of Sensitivity to Taxon Sampling.Molecular biology and evolution · 2023Review
- Four principles to establish a universal virus taxonomy.PLoS biology · 2023Article
- Metagenomic Analysis Using Phylogenetic Placement-A Review of the First Decade.Frontiers in bioinformatics · 2022Review
- Growth of Biological Complexity from Prokaryotes to Hominids Reflected in the Human Genome.International journal of molecular sciences · 2021Article
- PhyloMagnet: fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics.Bioinformatics (Oxford, England) · 2020Article
- Article
- Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences.Bioinformatics (Oxford, England) · 2019Article
- From De Novo to "De Nono": The Majority of Novel Protein-Coding Genes Identified with Phylostratigraphy Are Old Genes or Recent Duplicates.Genome biology and evolution · 2018Article
- Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogentic Tree of the Paniceae Grasses.Scientific reports · 2017Article
- OrthoReD: a rapid and accurate orthology prediction tool with low computational requirement.BMC bioinformatics · 2017Article
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2 authors.
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Abstract
Sequence similarity tools like Basic Local Alignment Search Tool (BLAST) are essential components of many functional genetic, genomic, phylogenetic and bioinformatic studies. Many modern analysis pipelines use significant sequence similarity scores (p- or E-values) and the ranked order of BLAST matches to test a wide range of hypotheses concerning homology, orthology, the timing of de novo gene birth/death and gene family expansion/contraction. Despite significant contrary findings, many of these tests still implicitly assume that stronger or higher-ranked E-value scores imply closer phylogenetic relationships between sequences. Here, we demonstrate that even though a general relationship does exist between the phylogenetic distance of two sequences and their E-value, significant and misleading errors occur in both the completeness and the order of results under realistic evolutionary scenarios. These results provide additional details to past evidence showing that studies should avoid drawing direct inferences of evolutionary relatedness from measures of sequence similarity alone, and should instead, where possible, use more rigorous phylogeny-based methods.
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