ArticleAlgorithms for molecular biology : AMB2018
Split-inducing indels in phylogenomic analysis.
Article in Algorithms for molecular biology : AMB, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed, 17 citations in OpenAlex.
- Genomic and epidemiological characterization of SARS-CoV-2 in Northeastern Brazil: a comprehensive analysis (2020-2024).Archives of virology · 2025Article
- Genetic diversity and origin of Kazakh Tobet Dogs.Scientific reports · 2024Article
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- Tatajuba: exploring the distribution of homopolymer tracts.NAR genomics and bioinformatics · 2022Article
- Article
- BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more.Applications in plant sciencesArticle
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Authors and funding
2 authors at 2 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMost phylogenetic studies using molecular data treat gaps in multiple sequence alignments as missing data or even completely exclude alignment columns that contain gaps.
resultsHere we show that gap patterns in large-scale, genome-wide alignments are themselves phylogenetically informative and can be used to infer reliable phylogenies provided the gap data are properly filtered to reduce noise introduced by the alignment method. We introduce here the notion of split-inducing indels (
conclusionsSuitably processed gap patterns extracted from genome-wide alignment provide a surprisingly clear phylogenetic signal and an allow the inference of accurate phylogenetic trees.
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