ArticleSystematic biology2019
Multiple Sequence Alignment Averaging Improves Phylogeny Reconstruction.
Article in Systematic biology, 2019. 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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Who cites it
15 citing papers in PubMed, 40 citations in OpenAlex.
- Resurrecting Full-Length Ancestral Schizorhodopsins and Heliorhodopsins with Structure-Guided, Indel-Aware Sequence Reconstruction.ACS omega · 2026Article
- PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space.BMC genomics · 2026Article
- Practical Guide and Review of Fossil Tip-Dating in Phylogenetics.Systematic biology · 2026Review
- Microbial Communities and Physicochemical Properties of the Nile River Water in the Suez Canal Area.Microorganisms · 2025Article
- Virome analysis and detection of ticks and tick-borne viruses in Shanghai, China.Frontiers in microbiology · 2025Article
- Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications.Molecular biology and evolution · 2024Review
- Common Methods for Phylogenetic Tree Construction and Their Implementation in R.Bioengineering (Basel, Switzerland) · 2024Review
- Incongruence in the phylogenomics era.Nature reviews. Genetics · 2023Review
- Article
- Relative model selection of evolutionary substitution models can be sensitive to multiple sequence alignment uncertainty.BMC ecology and evolution · 2021Article
- Molecular and Morphological Data Improve the Classification of Plantagineae (Lamiales).Plants (Basel, Switzerland) · 2021Article
- Article
- A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics.NAR genomics and bioinformatics · 2020Article
- First Phylogeny of Bitterbush Family, Picramniaceae (Picramniales).Plants (Basel, Switzerland) · 2020Article
- Animal Disease Surveillance in the 21st Century: Applications and Robustness of Phylodynamic Methods in Recent U.S. Human-Like H3 Swine Influenza Outbreaks.Frontiers in veterinary science · 2020Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
Abstract
The classic methodology of inferring a phylogenetic tree from sequence data is composed of two steps. First, a multiple sequence alignment (MSA) is computed. Then, a tree is reconstructed assuming the MSA is correct. Yet, inferred MSAs were shown to be inaccurate and alignment errors reduce tree inference accuracy. It was previously proposed that filtering unreliable alignment regions can increase the accuracy of tree inference. However, it was also demonstrated that the benefit of this filtering is often obscured by the resulting loss of phylogenetic signal. In this work we explore an approach, in which instead of relying on a single MSA, we generate a large set of alternative MSAs and concatenate them into a single SuperMSA. By doing so, we account for phylogenetic signals contained in columns that are not present in the single MSA computed by alignment algorithms. Using simulations, we demonstrate that this approach results, on average, in more accurate trees compared to 1) using an unfiltered MSA and 2) using a single MSA with weights assigned to columns according to their reliability. Next, we explore in which regions of the MSA space our approach is expected to be beneficial. Finally, we provide a simple criterion for deciding whether or not the extra effort of computing a SuperMSA and inferring a tree from it is beneficial. Based on these assessments, we expect our methodology to be useful for many cases in which diverged sequences are analyzed. The option to generate such a SuperMSA is available at http://guidance.tau.ac.il.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.