cognac: rapid generation of concatenated gene alignments for phylogenetic inference from large whole genome sequencing datasets
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AbstractThe quantity of genomic data is expanding at an increasing rate. Tools for phylogenetic analysis which scale to the quantity of available data are required. We present cognac, a user-friendly software package to rapidly generate concatenated gene alignments for phylogenetic analysis. We applied this tool to generate core gene alignments for very large genomic datasets, including a dataset of over 11,000 genomes from the genus Escherichia containing 1,353 genes, which was constructed in less than 17 hours. 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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2020 ◽
Vol 37
(5)
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pp. 1530-1534
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2020 ◽
Vol 35
(4)
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pp. 237-242
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