ArticleGenes2022
paPAML: An Improved Computational Tool to Explore Selection Pressure on Protein-Coding Sequences.
Article in Genes, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Retention of a single Cenp-C gene in different syntenic locations in the montium group of Drosophila species.Heredity · 2026Article
- Natural Selection Drives AT-Biased Codon Usage in Mitochondrial Genomes of Early-DivergingJournal of fungi (Basel, Switzerland) · 2026Article
- Transposable elements contribute to the evolution of host shift-related genes in cactophilicGenome research · 2026Article
- First Report of Human Infection Caused by Aspergillus steynii and Analysis of Its Whole-Genome Characteristics.Transboundary and emerging diseases · 2026Article
- Article
- Linking phenotype to genotype using comprehensive genomic comparisons.Current opinion in genetics & development · 2025Review
- Diversification and recurrent adaptation of the synaptonemal complex in Drosophila.PLoS genetics · 2025Article
- AlexandrusPS: A User-Friendly Pipeline for the Automated Detection of Orthologous Gene Clusters and Subsequent Positive Selection Analysis.Genome biology and evolution · 2023Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Evolution is change over time. Although neutral changes promoted by drift effects are most reliable for phylogenetic reconstructions, selection-relevant changes are of only limited use to reconstruct phylogenies. On the other hand, comparative analyses of neutral and selected changes of protein-coding DNA sequences (CDS) retrospectively tell us about episodic constrained, relaxed, and adaptive incidences. The ratio of sites with nonsynonymous (amino acid altering) versus synonymous (not altering) mutations directly measures selection pressure and can be analysed by using the Phylogenetic Analysis by Maximum Likelihood (PAML) software package. We developed a CDS extractor for compiling protein-coding sequences (CDS-extractor) and parallel PAML (paPAML) to simplify, amplify, and accelerate selection analyses via parallel processing, including detection of negatively selected sites. paPAML compiles results of site, branch-site, and branch models and detects site-specific negative selection with the output of a codon list labelling significance values. The tool simplifies selection analyses for casual and inexperienced users and accelerates computing speeds up to the number of allocated computer threads. We then applied paPAML to examine the evolutionary impact on a new GINS Complex Subunit 3 exon, and neutrophil-associated as well as lysin and apolipoprotein genes. Compared with codeml (PAML version 4.9j) and HyPhy (HyPhy FEL version 2.5.26), all paPAML test runs performed with 10 computing threads led to identical selection pressure results, whereas the total selection analysis via paPAML, including all model comparisons, was about 3 to 5 times faster than the longest running codeml model and about 7 to 15 times faster than the entire processing time of these codeml runs.
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Registered trials
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