ArticleGenome biology2010
Phylogenetic assessment of alignments reveals neglected tree signal in gaps.
Article in Genome biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed.
- Karyotype Variation and Environmental Adaptation in the Invasive Alien Freshwater FlatwormEcology and evolution · 2026Article
- AmpliPhy improves gene trees by adding homologous sequences without affecting alignments.Bioinformatics advances · 2026Article
- Exploring SNP filtering strategies: the influence of strict vs soft core.Microbial genomics · 2025Article
- Article
- Single-character insertion-deletion model preserves long indels in ancestral sequence reconstruction.BMC bioinformatics · 2024Article
- Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications.Molecular biology and evolution · 2024Review
- Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment Including Long Indels.Molecular biology and evolution · 2024Article
- Optimal phylogenetic reconstruction of insertion and deletion events.Bioinformatics (Oxford, England) · 2024Article
- Phylogenomics of the Ecdysteroid Kinase-like (EcKL) Gene Family in Insects Highlights Roles in Both Steroid Hormone Metabolism and Detoxification.Genome biology and evolution · 2024Article
- Article
- ARPIP: Ancestral Sequence Reconstruction with Insertions and Deletions under the Poisson Indel Process.Systematic biology · 2023Article
- The difficulty of aligning intrinsically disordered protein sequences as assessed by conservation and phylogeny.PloS one · 2023Article
- The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics.GigaScience · 2022Article
- Highly significant improvement of protein sequence alignments with AlphaFold2.Bioinformatics (Oxford, England) · 2022Article
- Insertions and deletions as phylogenetic signal in an alignment-free context.PLoS computational biology · 2022Article
- Article
- Measuring Phylogenetic Information of Incomplete Sequence Data.Systematic biology · 2022Article
- Phylogenetic survey of the subtilase family and a data-mining-based search for new subtilisins fromFrontiers in microbiology · 2022Article
- Comparative analysis of the chloroplast genomes of eightFrontiers in genetics · 2022Article
- No hybrid snowcocks in the Altai-Hyper-variable markers can be problematic for phylogenetic inference.Ecology and evolution · 2021Article
4 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe alignment of biological sequences is of chief importance to most evolutionary and comparative genomics studies, yet the two main approaches used to assess alignment accuracy have flaws: reference alignments are derived from the biased sample of proteins with known structure, and simulated data lack realism.
resultsHere, we introduce tree-based tests of alignment accuracy, which not only use large and representative samples of real biological data, but also enable the evaluation of the effect of gap placement on phylogenetic inference. We show that (i) the current belief that consistency-based alignments outperform scoring matrix-based alignments is misguided; (ii) gaps carry substantial phylogenetic signal, but are poorly exploited by most alignment and tree building programs; (iii) even so, excluding gaps and variable regions is detrimental; (iv) disagreement among alignment programs says little about the accuracy of resulting trees.
conclusionsThis study provides the broad community relying on sequence alignment with important practical recommendations, sets superior standards for assessing alignment accuracy, and paves the way for the development of phylogenetic inference methods of significantly higher resolution.
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