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GWideCodeML: A Python Package for Testing Evolutionary Hypotheses at the Genome-Wide Level by Macías, Laura G.; Barrio, Eladio; Toft, Christina is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

What is GWideCodeML: A Python Package for Testing Evolutionary Hypotheses at the Genome-Wide Level about?

## Abstract One of the most widely used programs for detecting positive selection, at the molecular level, is the program codeml, which is implemented in the Phylogenetic Analysis by Maximum Likelihood (PAML) package. However, it has a limitation when it comes to genome-wide studies, as it runs on a gene-by-gene basis. Furthermore, the size of such studies will depend on the number of orthologous genes the genomes have income and these are often restricted to only account for instances where a one-to-one relationship is observed between the genomes. In this work, we present GWideCodeML, a Python package, which runs a genome-wide codeml with the option of parallelization. To maximize the number of analyzed genes, the package allows for a variable number of taxa in the alignments and will automatically prune the topology to fit each of them, before running codeml.

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Author

Macías, Laura G.; Barrio, Eladio; Toft, Christina

Publisher

The Genetics Society of America; Genetics Society of America; Bethesda MD: Genetics Society of America, 2011-; Oxford University Press (OUP) (ISSN 2160-1836)

Published

2020

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)