Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies

Spielman, Scott R.; Wilke, Claus O.

doi:10.1101/020214

Cited by 3 publications

(1 citation statement)

References 51 publications

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“…the R package phangorn, Schliep 2011; the python module pyvolve, Sipos et al . 2011; the R package phylosim, Spielman & Wilke 2015) provide algorithms to simulate sequence evolution along the branches of the phylogeny, given a rooted phylogeny and a root sequence (e.g. some arbitrary sequence assumed to represent the ancestral sequence), by applying the transition matrix sequentially along the phylogenetic tree.…”

Section: Methodsmentioning

confidence: 99%

Nucleotide substitutions during speciation may explain substitution rate variation

Janzen

Bokma

Etienne

2020

Preprint

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Although molecular mechanisms associated with the generation of mutations are highly conserved across taxa, there is widespread variation in mutation rates between evolutionary lineages. When phylogenies are reconstructed based on nucleotide sequences, such variation is typically accounted for by the assumption of a relaxed molecular clock, which, however, is just a statistical distribution of mutation rates without any underlying biological mechanism. Here, we propose that variation in accumulated mutations may be partly explained by an elevated mutation rate during speciation. Using simulations, we show how shifting mutations from branches to speciation events impacts inference of branching times in phylogenetic reconstruction. Furthermore, the resulting nucleotide alignments are better described by a relaxed than by a strict molecular clock. Thus, elevated mutation rates during speciation potentially explain part of the variation in substitution rates that is observed across the tree of life.

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Section: Methodsmentioning

confidence: 99%

Nucleotide substitutions during speciation may explain substitution rate variation

Janzen

Bokma

Etienne

2020

Preprint

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Accurate prediction of site- and amino-acid substitution rates with a mutation-selection model

André

2024

Preprint

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The pattern of substitutions at sites in proteins provides invaluable information about their biophysical and functional importance and what selection pressures are acting at individual sites. Amino acid site rates are typically estimated using phenomenological models in which the sequence variability is described by rate factors that scale the overall substitution rate in a protein to sites. In this study, we demonstrate that site rates can be calculated accurately from amino acid sequences using a mutation-selection model in combination with a simple nucleotide substitution model. The method performs better than the standard phylogenetic approach on sequences generated by structure-based evolutionary dynamics simulations, robustly estimates rates for shallow multiple sequence alignments, and can be rapidly calculated also on larger sequence alignments. On natural sequences, site rates from the mutation-selection model are strongly correlated to rates calculated with the empirical Bayes methods. The model provides a link between amino acid substitution rates and equilibrium frequency distributions at sites in proteins. We show how an ensemble of equilibrium frequency vectors can be used to represent the rate variation encoded in empirical amino acid substitution matrices. This study demonstrates that a rapid and simple method can be developed from the mutation-selection model to predict substitution rates from amino acid data, complementing the standard phylogenetic approach.

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AsymmeTree: A Flexible Python Package for the Simulation of Complex Gene Family Histories

2022

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AsymmeTree is a flexible and easy-to-use Python package for the simulation of gene family histories. It simulates species trees and considers the joint action of gene duplication, loss, conversion, and horizontal transfer to evolve gene families along the species tree. To generate realistic scenarios, evolution rate heterogeneity from various sources is modeled. Finally, nucleotide or amino acid sequences (optionally with indels, among-site rate heterogeneity, and invariant sites) can be simulated along the gene phylogenies. For all steps, users can choose from a spectrum of alternative methods and parameters. These choices include most options that are commonly used in comparable tools but also some that are usually not found, such as the innovation model for species evolution. While output files for each individual step can be generated, AsymmeTree is primarily intended to be integrated in complex Python pipelines designed to assess the performance of data analysis methods. It allows the user to interact with, analyze, and possibly manipulate the simulated scenarios. AsymmeTree is freely available on GitHub.

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Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies

Cited by 3 publications

References 51 publications

Nucleotide substitutions during speciation may explain substitution rate variation

Nucleotide substitutions during speciation may explain substitution rate variation

Accurate prediction of site- and amino-acid substitution rates with a mutation-selection model

AsymmeTree: A Flexible Python Package for the Simulation of Complex Gene Family Histories

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