HiMAP2: Identifying phylogenetically informative genetic markers from diverse genomic resources DOI
Oksana Vernygora, Carlos Congrains, Scott M. Geib

и другие.

Molecular Ecology Resources, Год журнала: 2023, Номер 23(5), С. 1155 - 1167

Опубликована: Фев. 2, 2023

Multiplexed amplicon sequencing offers a cost-effective and rapid solution for phylogenomic studies that include large number of individuals. Selecting informative genetic markers is critical initial step in designing such multiplexed panels, but screening various genomic data selecting are the question at hand can be laborious. Here, we present flexible user-friendly tool, HiMAP2, identifying, visualizing filtering phylogenetically loci from diverse transcriptomic resources. This bioinformatics pipeline includes orthology prediction, exon extraction aligned sequences according to user-defined specifications. Additionally, HiMAP2 facilitates exploration final filtered exons by incorporating phylogenetic inference individual trees with raxml-ng as well estimation species tree using astral. Finally, results marker selection visualized refined an interactive Bokeh application used generate publication-quality figures. Source code user instructions available https://github.com/popphylotools/HiMAP_v2.

Язык: Английский

HiMAP2: Identifying phylogenetically informative genetic markers from diverse genomic resources DOI
Oksana Vernygora, Carlos Congrains, Scott M. Geib

и другие.

Molecular Ecology Resources, Год журнала: 2023, Номер 23(5), С. 1155 - 1167

Опубликована: Фев. 2, 2023

Multiplexed amplicon sequencing offers a cost-effective and rapid solution for phylogenomic studies that include large number of individuals. Selecting informative genetic markers is critical initial step in designing such multiplexed panels, but screening various genomic data selecting are the question at hand can be laborious. Here, we present flexible user-friendly tool, HiMAP2, identifying, visualizing filtering phylogenetically loci from diverse transcriptomic resources. This bioinformatics pipeline includes orthology prediction, exon extraction aligned sequences according to user-defined specifications. Additionally, HiMAP2 facilitates exploration final filtered exons by incorporating phylogenetic inference individual trees with raxml-ng as well estimation species tree using astral. Finally, results marker selection visualized refined an interactive Bokeh application used generate publication-quality figures. Source code user instructions available https://github.com/popphylotools/HiMAP_v2.

Язык: Английский

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