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bioRxiv · 10.1101/2020.10.15.340901

cognac: rapid generation of concatenated gene alignments for phylogenetic inferencefrom large whole genome sequencing datasets

Snitkin, E. S.·Crawford, R. D.
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Abstract

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. 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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Snitkin, E. S., Crawford, R. D.. 2020-10-15. cognac: rapid generation of concatenated gene alignments for phylogenetic inferencefrom large whole genome sequencing datasets. https://doi.org/10.1101/2020.10.15.340901

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