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Grid selection of models of nucleotide substitution

Marta Loureiro, Miguel Pan, Manuel Rodríguez-Pascual, David Posada, Rafael Mayo
2010 Studies in Health Technology and Informatics  
jModelTest is a Java program for the statistical selection of models of nucleotide substitution with thousands of users around the world.  ...  Here we describe the port of the jModeltest code for Grid computing using DRMAA. This work should facilitate the use of jModelTest on a broad scale.  ...  An essential step of the phylogenetic analysis is the selection of appropriate models of nucleotide substitution [1] .  ... 
pmid:20543444 pmcid:PMC4961237 fatcat:rrvodjnqrbcftnbtfnetw23j5m

Annotation of selection strengths in viral genomes

Stephen McCauley, Saskia de Groot, Thomas Mailund, Jotun Hein
2007 Computer applications in the biosciences : CABIOS  
To the best of our knowledge, we are the first to subsequently provide a full selection annotation of the Hepatitis B genome by explicitly modelling the evolution within overlapping reading frames, and  ...  We introduce an evolutionary model capable of accounting for varying levels of selection along the genome, and incorporate it into our prior single sequence HMM methodology, extending it now to a phylogenetic  ...  Without the autocorrelation, but keeping the grid of selection factors, we would essentially be modelling selection as a mixture model, similar to Yang and Swanson (2002) .  ... 
doi:10.1093/bioinformatics/btm472 pmid:17921171 fatcat:pzluqel5obbdbf4u6mx3pz3vui

FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection

B. Murrell, S. Moola, A. Mabona, T. Weighill, D. Sheward, S. L. Kosakovsky Pond, K. Scheffler
2013 Molecular biology and evolution  
Model-based analyses of natural selection often categorize sites into a relatively small number of site classes.  ...  Forcing each site to belong to one of these classes places unrealistic constraints on the distribution of selection parameters, which can result in misleading inference due to model misspecification.  ...  Research Foundation of South Africa, the University of Cape Town's University Research Council, and Europeaid grant SANTE/2007/147-790 from the European Commission.  ... 
doi:10.1093/molbev/mst030 pmid:23420840 pmcid:PMC3670733 fatcat:fpsahwgwrfekdbhtwkxxhy2vlq

Protein Evolution with Dependence Among Codons Due to Tertiary Structure

D. M. Robinson
2003 Molecular biology and evolution  
By explicitly considering the relationship between nonsynonymous substitution rates and protein structure, this approach can lead to refined detection and characterization of positive selection.  ...  Markovian models of protein evolution that relax the assumption of independent change among codons are considered.  ...  For this site, we base the sampling of the proposed site path q9 r on a simple model of evolution that assumes independence of nucleotide substitutions among sites.  ... 
doi:10.1093/molbev/msg184 pmid:12885968 fatcat:apg7qzccjves5phv7bchargrmu

Nucleotide substitutions in dengue virus serotypes from Asian and American countries: insights into intracodon recombination and purifying selection

Susanta K Behura, David W Severson
2013 BMC Microbiology  
We show that fixation of nucleotide substitutions is more prominent among the inter-continental isolates (Asian and American) of serotypes 1, 2 and 3 compared to serotype 4 isolates (South and Central  ...  Results: We investigated genome-wide genetic diversity and nucleotide substitution patterns in the four serotypes among samples collected from different countries in Asia and Central and South America  ...  Mathew Henn, Broad Institute of MIT & Harvard, Cambridge for allowing us to use the GRID data and Dr. Mabel Berois for critical reading of the manuscript.  ... 
doi:10.1186/1471-2180-13-37 pmid:23410119 pmcid:PMC3598932 fatcat:wwr57aycsvbxtj35myazntahoa

A thermodynamic model of protein structure evolution explains empirical amino acid substitution matrices

Christoffer Norn, Ingemar André, Douglas L. Theobald
2021 Protein Science  
Proteins evolve under a myriad of biophysical selection pressures that collectively control the patterns of amino acid substitutions.  ...  This hybrid biophysical and evolutionary model accounts for nucleotide transition/transversion rate bias, multi-nucleotide codon changes, the number of codons per amino acid, and thermodynamic protein  ...  A global amino acid substitution matrix can then be constructed from these amino acid fixation probabilities and a codon-level model of nucleotide mutation.  ... 
doi:10.1002/pro.4155 pmid:34218472 pmcid:PMC8442976 fatcat:626efhku35a23hlwd6yinnyzxi

jmodeltest.org: selection of nucleotide substitution models on the cloud

J. M. Santorum, D. Darriba, G. L. Taboada, D. Posada
2014 Bioinformatics  
The selection of models of nucleotide substitution is one of the major steps of modern phylogenetic analysis.  ...  Here we present jmodeltest.org, a novel web server for the transparent execution of jMT2 across different platforms and for a wide range of users.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btu032 pmid:24451621 pmcid:PMC3998143 fatcat:4xq7wuafibeubcdul6otq3u2ay

Bayesian Selection of Nucleotide Substitution Models and Their Site Assignments

Chieh-Hsi Wu, Marc A. Suchard, Alexei J. Drummond
2012 Molecular biology and evolution  
substitution model for each partition, and the uncertainty in these selections.  ...  We find that this approach dramatically improves the fit of the nucleotide substitution model compared with existing approaches, and we show, using a number of example data sets, that as many as nine partitions  ...  .), a University of Auckland Doctoral Scholarship (to C.-H.W.) and NIH R01 GM086887 and R01 HG006139.  ... 
doi:10.1093/molbev/mss258 pmid:23233462 pmcid:PMC3563969 fatcat:gwqa3gphjnaw3eoo36jzv7p4fq

TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops

I. Milne, D. Lindner, M. Bayer, D. Husmeier, G. McGuire, D. F. Marshall, F. Wright
2008 Bioinformatics  
of the tree and the substitution model.  ...  The optimal substitution model can be selected for protein or nucleic acid (standard, or protein-coding using a codon position model) data using accurate statistical criteria derived from ML co-estimation  ...  Model selection: the menu launches models available in MrBayes (24 nucleotide models, 36 amino acid models) or in PhyML (56 and 40, respectively) or in RAxML (no nucleotide model choice, 40 amino acid  ... 
doi:10.1093/bioinformatics/btn575 pmid:18984599 pmcid:PMC2638937 fatcat:ymvgx4hs5zfbtefdpq45fxwloi

MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment

S. Kumar
2004 Briefings in Bioinformatics  
species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes.  ...  Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary  ...  Their comments influenced and improved all facets of user interface and methodology implementation.  ... 
doi:10.1093/bib/5.2.150 pmid:15260895 fatcat:nmi5opa5zzex5lwfq63q4zciyy

Modular Organization of Residue-Level Contacts Shapes the Selection Pressure on Individual Amino Acid Sites of Ribosomal Proteins

Saurav Mallik, Sudip Kundu
2017 Genome Biology and Evolution  
Amino acid-nucleotide constituents of OaantCs with higher contact numbers are generally associated with significantly slower substitution rates compared with that of OaantCs with smaller contact numbers  ...  Contact number is defined as the number of nucleotides contacted.  ...  This work is supported by the Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase II), University of Calcutta, India.  ... 
doi:10.1093/gbe/evx036 pmid:28338825 pmcid:PMC5388290 fatcat:fpqrwhbekjejvkzr3v4j7byy2e

A thermodynamic model of protein structure evolution explains empirical amino acid rate matrices [article]

Christoffer Norn, Ingemar Andre, Douglas L Theobald
2020 bioRxiv   pre-print
Proteins evolve under a myriad of biophysical selection pressures that collectively control the patterns of amino acid substitutions.  ...  This hybrid biophysical and evolutionary model accounts for nucleotide transition/transversion rate bias, multi-nucleotide codon changes, the number of codons per amino acid, and thermodynamic protein  ...  A global amino acid substitution matrix can then be constructed from these amino acid fixation probabilities and a codon-level model of nucleotide mutation.  ... 
doi:10.1101/2020.12.02.408807 fatcat:zs3bjm5345gddb3v5frmuuqnne

Dependence among Sites in RNA Evolution

Jiaye Yu, Jeffrey L. Thorne
2006 Molecular biology and evolution  
The underlying idea is that a nucleotide substitution resulting in a more stable secondary structure should have a higher rate than a substitution that yields a less stable secondary structure.  ...  Although probabilistic models of genotype (e.g., DNA sequence) evolution have been greatly elaborated, less attention has been paid to the effect of phenotype on the evolution of the genotype.  ...  This work was partially supported by National Science Foundation DEB-0445180 and National Institutes of Health R01 GM070806 to J.L.T. and by a Danish National Science Foundation grant to Rasmus Nielsen  ... 
doi:10.1093/molbev/msl015 pmid:16720696 fatcat:i7yurvdxpfc4xmrhn5b4ejtdde

Modern Technologies Used for Security of Software Applications [chapter]

Tatiana Hodorogea, Ionas Szilard
2012 Applied Cryptography and Network Security  
models.  ...  Our work is based on Deriving DNA Cryptographic Keys Based on Evolutionary Models for Security of Software Applications.  ...  The foreground model I assume that, at a given position i, the substitution rates r i i w   are altered due to specific selection preferences for certain bases at this position, parameterized by nucleotide  ... 
doi:10.5772/34013 fatcat:kwxpe2sisfh6hkk7ylz7csearq

Evolution of Disease Response Genes in Loblolly Pine: Insights from Candidate Genes

Elhan S. Ersoz, Mark H. Wright, Santiago C. González-Martínez, Charles H. Langley, David B. Neale, Simon Joly
2010 PLoS ONE  
Methodology/Principal Findings: Here, we present nucleotide polymorphism and substitution data for 41 candidate genes from the long-lived forest tree loblolly pine, selected primarily for their prospective  ...  and erd3 (early response to drought 3) displays patterns suggestive of a selective sweep, both of which are consistent with the arm-race model of disease response evolution.  ...  Garth Brown for his help and contribution at early stages of this study. We also would like to thank the communicating editor Dr. Simon Joly and reviewers of the manuscript Dr.  ... 
doi:10.1371/journal.pone.0014234 pmid:21151911 pmcid:PMC2997792 fatcat:fjnsfdy3jzgznnfg52eci56uq4
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