INDELible: a flexible simulator of biological sequence evolution.
William Fletcher,Ziheng Yang +1 more
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TLDR
A portable and flexible application for generating nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions, which should be useful for evaluating the performance of many inference methods, including those for multiple sequence alignment, phylogenetic tree inference, and ancestral sequence, or genome reconstruction.Abstract:
Many methods exist for reconstructing phylogenies from molecular sequence data, but few phylogenies are known and can be used to check their efficacy. Simulation remains the most important approach to testing the accuracy and robustness of phylogenetic inference methods. However, current simulation programs are limited, especially concerning realistic models for simulating insertions and deletions. We implement a portable and flexible application, named INDELible, for generating nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. Indels are simulated under several models of indel-length distribution. The program implements a rich repertoire of substitution models, including the general unrestricted model and nonstationary nonhomogeneous models of nucleotide substitution, mixture, and partition models that account for heterogeneity among sites, and codon models that allow the nonsynonymous/synonymous substitution rate ratio to vary among sites and branches. With its many unique features, INDELible should be useful for evaluating the performance of many inference methods, including those for multiple sequence alignment, phylogenetic tree inference, and ancestral sequence, or genome reconstruction.read more
Citations
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Kazutaka Katoh,Daron M. Standley +1 more
TL;DR: This version of MAFFT has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update.
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ModelFinder: fast model selection for accurate phylogenetic estimates
Subha Kalyaanamoorthy,Subha Kalyaanamoorthy,Bui Quang Minh,Thomas K. F. Wong,Thomas K. F. Wong,Arndt von Haeseler,Arndt von Haeseler,Lars S. Jermiin,Lars S. Jermiin +8 more
TL;DR: ModelFinder is presented, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.
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A general species delimitation method with applications to phylogenetic placements
TL;DR: The Poisson tree processes (PTP) model is introduced to infer putative species boundaries on a given phylogenetic input tree and yields more accurate results than de novo species delimitation methods.
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ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees.
TL;DR: ASTRAL-III is a faster version of the ASTRAL method for phylogenetic reconstruction and can scale up to 10,000 species and removes low support branches from gene trees, resulting in improved accuracy.
References
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TL;DR: Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.
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Exact Stochastic Simulation of Coupled Chemical Reactions
TL;DR: In this article, a simulation algorithm for the stochastic formulation of chemical kinetics is proposed, which uses a rigorously derived Monte Carlo procedure to numerically simulate the time evolution of a given chemical system.
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Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.
Koichiro Tamura,Masatoshi Nei +1 more
TL;DR: In this paper, a new mathematical method for estimating the number of transitional and transversional substitutions per site, as well as the total number of nucleotide substitutions was proposed, taking into account excess transitions, unequal nucleotide frequencies, and variation of substitution rate among different sites.