ArticleSystematic biology2016
Maximum Likelihood Phylogenetic Inference is Consistent on Multiple Sequence Alignments, with or without Gaps.
Article in Systematic biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Decoding the Evolution and Co-Phospho-Regulatory Networks of SHROOM Proteins.Journal of molecular evolution · 2026Article
- An Introduction to Structural Phylogenetics for Biomedical Sciences.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Protein Structural Phylogenetics.Genome biology and evolution · 2025Review
- Functional characterization of Cullin-1-RING ubiquitin ligase (CRL1) complex in Leishmania infantum.PLoS pathogens · 2024Article
- The role of prickle proteins in vertebrate development and pathology.Molecular and cellular biochemistry · 2024Review
- New Insights into Hop Latent Viroid Detection, Infectivity, Host Range, and Transmission.Viruses · 2023Article
- Genome-Wide Identification and Functional Characterization ofPlants (Basel, Switzerland) · 2023Article
- Evolution of the Immunoglobulin Isotypes-Variations of Biophysical Properties among Animal Classes.Biomolecules · 2023Article
- Evolution of the Inhibitory and Non-Inhibitory ε, ζ, and IFMicroorganisms · 2022Review
- Genome-Wide Identification and Expression Analysis of Homeodomain Leucine Zipper Subfamily IV (HD-ZIP IV) Gene Family inPlants (Basel, Switzerland) · 2022Article
- SufB intein splicing in Mycobacterium tuberculosis is influenced by two remote conserved N-extein histidines.Bioscience reports · 2022Article
- Characterization and expression profiling of PIN auxin efflux transporters reveal their role in developmental and abiotic stress conditions in rice.Frontiers in plant science · 2022Article
- Phylogeny Estimation Given Sequence Length Heterogeneity.Systematic biology · 2021Article
- Article
- Accurate Inference of Tree Topologies from Multiple Sequence Alignments Using Deep Learning.Systematic biology · 2020Article
- Article
- A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions.PeerJ · 2018Article
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2 authors.
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Abstract
We prove that maximum likelihood phylogenetic inference is consistent on gapped multiple sequence alignments (MSAs) as long as substitution rates across each edge are greater than zero, under mild assumptions on the structure of the alignment. Under these assumptions, maximum likelihood will asymptotically recover the tree with edge lengths corresponding to the mean number of substitutions per site on each edge. This refutes Warnow's recent suggestion (Warnow 2012) that maximum likelihood phylogenetic inference might be statistically inconsistent when gaps are treated as missing data, even if the MSA is correct. We also derive a simple new proof of maximum likelihood consistency of ungapped alignments.
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