期刊
BMC BIOINFORMATICS
卷 22, 期 1, 页码 -出版社
BMC
DOI: 10.1186/s12859-021-03981-4
关键词
Concatenated gene tree; Core genome; Multiple sequence alignment; Phylogenetics
类别
资金
- University of Michigan Bioinformatics Training Grant [T32 GM070449]
- NIH RO1 [1R01AI148259-01]
cognac is a user-friendly software package for rapidly generating concatenated gene alignments for phylogenetic analysis, which can quickly identify phylogenetic marker genes using a data-driven approach. The tool efficiently generates concatenated gene alignments for very large genomic datasets in a short amount of time.
Background: The quantity of genomic data is expanding at an increasing rate. Tools for phylogenetic analysis which scale to the quantity of available data are required. To address this need, we present cognac, a user-friendly software package to rapidly generate concatenated gene alignments for phylogenetic analysis. Results: We illustrate that cognac is able to rapidly identify phylogenetic marker genes using a data driven approach and efficiently generate concatenated gene alignments for very large genomic datasets. To benchmark our tool, we generated core gene alignments for eight unique genera of bacteria, including a dataset of over 11,000 genomes from the genus Escherichia producing an alignment with 1353 genes, which was constructed in less than 17 h. Conclusions: We demonstrate that cognac presents an efficient method for generating concatenated gene alignments for phylogenetic analysis. We have released cognac as an R package (https://github.com/rdcrawford/cognac) with customizable parameters for adaptation to diverse applications.
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