PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data | Zendy

Jacob L. Steenwyk | Zendy; Thomas J. Buida | Zendy; Abigail L. LaBella | Zendy; Yuanning Li | Zendy; XingXing Shen | Zendy; Antonis Rokas | Zendy

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PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data

Author(s) -

Jacob L. Steenwyk,

Thomas J. Buida,

Abigail L. LaBella,

Yuanning Li,

XingXing Shen,

Antonis Rokas

Publication year - 2021

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btab096

Subject(s) - computer science , unix , phylogenetic tree , tree (set theory) , source code , phylogenomics , process (computing) , sequence (biology) , documentation , data mining , information retrieval , programming language , software , biology , gene , clade , mathematical analysis , biochemistry , genetics , mathematics

Diverse disciplines in biology process and analyze multiple sequence alignments (MSAs) and phylogenetic trees to evaluate their information content, infer evolutionary events and processes and predict gene function. However, automated processing of MSAs and trees remains a challenge due to the lack of a unified toolkit. To fill this gap, we introduce PhyKIT, a toolkit for the UNIX shell environment with 30 functions that process MSAs and trees, including but not limited to estimation of mutation rate, evaluation of sequence composition biases, calculation of the degree of violation of a molecular clock and collapsing bipartitions (internal branches) with low support.

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