ArticleBMC bioinformatics2021
P*R*O*P: a web application to perform phylogenetic analysis considering the effect of gaps.
Article in BMC bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Evaluation of Molecular Phylogenetic Trees by an Information-Theoretic Metric.Journal of molecular evolution · 2026Article
- Revisiting Algorithms, Tools, and Applications for Sequence and Phylogenetic Analyses in the NGS-Based Omics Era.Biochemical genetics · 2026Review
- A Prickly Problem: Genome Skimming Reveals Varying Levels of Phylogenetic Diversity in the Freshwater CrayfishEcology and evolution · 2026Article
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2 authors.
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Abstract
backgroundPhylogenetic analysis strongly depends on evolutionary models. Most evolutionary models for estimating genetic differences and phylogenetic relationships do not treat gap sites in the alignment of sequences. Appropriately incorporating evolutionary information of sites containing insertions and deletions into genetic difference measures will be improve the accuracy of phylogenetic estimates.
resultsWe introduced a new measure for estimating genetic differences, and presented P*R*O*P, a web application for performing phylogenetic analysis based on genetic difference considering the effect of gaps. As an example of phylogenetic analysis using P*R*O*P, we used complete p53 amino acid sequences of 31 organisms and illustrated that the genetic differences with and without information on sites containing gaps result in trees with different topologies.
conclusionsP*R*O*P is available at https://www.rs.tus.ac.jp/bioinformatics/prop and the user can perform phylogenetic analysis by uploading sequence data on the website. The most distinctive feature of P*R*O*P is its genetic difference that is estimated without eliminating gap sites for alignment sequences, which helps users detect meaningful difference in an evolutionary process. The source code is available in GitHub: https://github.com/TUS-Satolab/PROP .
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