ArticleProceedings of the National Academy of Sciences of the United States of America2013
Evolutionary inference via the Poisson Indel Process.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Efficient algorithms for simulating sequences along a phylogenetic tree.Bioinformatics (Oxford, England) · 2026Article
- Protein Structural Phylogenetics.Genome biology and evolution · 2025Review
- Algorithms to reconstruct past indels: The deletion-only parsimony problem.PLoS computational biology · 2025Article
- Impact of Phylogenetic Method Choice on Indel Analyses in HIV-1 Subtype B.Genome biology and evolution · 2025Article
- 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
- Statistical framework to determine indel-length distribution.Bioinformatics (Oxford, England) · 2024Article
- ARPIP: Ancestral Sequence Reconstruction with Insertions and Deletions under the Poisson Indel Process.Systematic biology · 2023Article
- Measuring Phylogenetic Information of Incomplete Sequence Data.Systematic biology · 2022Article
- Tatajuba: exploring the distribution of homopolymer tracts.NAR genomics and bioinformatics · 2022Article
- ProPIP: a tool for progressive multiple sequence alignment with Poisson Indel Process.BMC bioinformatics · 2021Article
- TRAL 2.0: Tandem Repeat Detection With Circular Profile Hidden Markov Models and Evolutionary Aligner.Frontiers in bioinformatics · 2021Article
- Article
- Accelerating phylogeny-aware alignment with indel evolution using short time Fourier transform.NAR genomics and bioinformatics · 2020Article
- On the reconstruction of the ancestral bacterial genomes in genus Mycobacterium and Brucella.BMC systems biology · 2018Article
- Progressive multiple sequence alignment with indel evolution.BMC bioinformatics · 2018Article
- The Bayesian optimist's guide to adaptive immune receptor repertoire analysis.Immunological reviews · 2018Review
- Solving the master equation for Indels.BMC bioinformatics · 2017Article
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2 authors.
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Abstract
We address the problem of the joint statistical inference of phylogenetic trees and multiple sequence alignments from unaligned molecular sequences. This problem is generally formulated in terms of string-valued evolutionary processes along the branches of a phylogenetic tree. The classic evolutionary process, the TKF91 model [Thorne JL, Kishino H, Felsenstein J (1991) J Mol Evol 33(2):114-124] is a continuous-time Markov chain model composed of insertion, deletion, and substitution events. Unfortunately, this model gives rise to an intractable computational problem: The computation of the marginal likelihood under the TKF91 model is exponential in the number of taxa. In this work, we present a stochastic process, the Poisson Indel Process (PIP), in which the complexity of this computation is reduced to linear. The Poisson Indel Process is closely related to the TKF91 model, differing only in its treatment of insertions, but it has a global characterization as a Poisson process on the phylogeny. Standard results for Poisson processes allow key computations to be decoupled, which yields the favorable computational profile of inference under the PIP model. We present illustrative experiments in which Bayesian inference under the PIP model is compared with separate inference of phylogenies and alignments.
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