Testing adequacy for DNA substitution models
نویسندگان
چکیده
منابع مشابه
MODELTEST: testing the model of DNA substitution
SUMMARY The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data. AVAILABILITY The MODELTEST package, including the source code and some documentation is available at http://bioag.byu. edu/zoology/crandall_lab/modeltest.html.
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The concomitantly variable codons hypothesis of DNA substitution argues that at any time only a fraction of the codons in a gene are capable of accepting a mutation. However, as mutations are fixed at some positions in a gene, the sites that are potentially variable also change because of changed functional constraints. This hypothesis has been termed the "covarion" hypothesis or when the model...
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Phylogenetic tree reconstruction frequently assumes the homogeneity of the substitution process over the whole tree. To test this assumption statistically, we propose a test based on the sample covariance matrix of the set of substitution rate matrices estimated from pairwise sequence comparison. The sample covariance matrix is condensed into a one-dimensional test statistic Delta = sum ln(1 + ...
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In this report, criteria for adequacy measurement for objects in OO software are presented. Coverage criteria that address internal object structure have been developed. These criteria include coverage of direct and indirect inter-method ows in addition to internal method control ows. Results from the analysis of a commercial system developed in C++ support the theory that coverage analysis bas...
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This paper presents the High Performance Computing (HPC) support of jModelTest2, the most popular bioinformatic tool for the statistical selection of models of DNA substitution. As this task can demand vast computational resources, especially in terms of processing power, jModelTest2 implements three parallel algorithms for model selection: (1) a multithreaded implementation for shared memory a...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2019
ISSN: 1471-2105
DOI: 10.1186/s12859-019-2905-3