ArticlePloS one2012
Accurate reconstruction of insertion-deletion histories by statistical phylogenetics.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- An Evolving View of Character Macroevolution.Systematic biology · 2026Review
- Deep models of protein evolution in time generate realistic evolutionary trajectories and functional proteins.bioRxiv : the preprint server for biology · 2026Article
- Impact of Phylogenetic Method Choice on Indel Analyses in HIV-1 Subtype B.Genome biology and evolution · 2025Article
- 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
- Machine Boss: rapid prototyping of bioinformatic automata.Bioinformatics (Oxford, England) · 2021Article
- Article
- Alignment Modulates Ancestral Sequence Reconstruction Accuracy.Molecular biology and evolution · 2018Article
- Solving the master equation for Indels.BMC bioinformatics · 2017Article
- Historian: accurate reconstruction of ancestral sequences and evolutionary rates.Bioinformatics (Oxford, England) · 2017Article
- General continuous-time Markov model of sequence evolution via insertions/deletions: local alignment probability computation.BMC bioinformatics · 2016Article
- General continuous-time Markov model of sequence evolution via insertions/deletions: are alignment probabilities factorable?BMC bioinformatics · 2016Article
- Characterization of multiple sequence alignment errors using complete-likelihood score and position-shift map.BMC bioinformatics · 2016Article
- Simultaneous Bayesian estimation of alignment and phylogeny under a joint model of protein sequence and structure.Molecular biology and evolution · 2014Article
- Phylogenetic quantification of intra-tumour heterogeneity.PLoS computational biology · 2014Article
- Evolutionary origins of a bioactive peptide buried within Preproalbumin.The Plant cell · 2014Article
- Graph-based modeling of tandem repeats improves global multiple sequence alignment.Nucleic acids research · 2013Article
- Evolutionary inference via the Poisson Indel Process.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Sequence context of indel mutations and their effect on protein evolution in a bacterial endosymbiont.Genome biology and evolution · 2013Article
- Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites.BMC bioinformatics · 2012Article
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Authors and funding
4 authors.
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Abstract
The Multiple Sequence Alignment (MSA) is a computational abstraction that represents a partial summary either of indel history, or of structural similarity. Taking the former view (indel history), it is possible to use formal automata theory to generalize the phylogenetic likelihood framework for finite substitution models (Dayhoff's probability matrices and Felsenstein's pruning algorithm) to arbitrary-length sequences. In this paper, we report results of a simulation-based benchmark of several methods for reconstruction of indel history. The methods tested include a relatively new algorithm for statistical marginalization of MSAs that sums over a stochastically-sampled ensemble of the most probable evolutionary histories. For mammalian evolutionary parameters on several different trees, the single most likely history sampled by our algorithm appears less biased than histories reconstructed by other MSA methods. The algorithm can also be used for alignment-free inference, where the MSA is explicitly summed out of the analysis. As an illustration of our method, we discuss reconstruction of the evolutionary histories of human protein-coding genes.
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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.