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cognac: rapid generation of concatenated gene alignments for phylogenetic inference from large whole genome sequencing datasets
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cognac: rapid generation of concatenated gene alignments for phylogenetic inference from large whole genome sequencing datasets
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Paper
cognac: rapid generation of concatenated gene alignments for phylogenetic inference from large whole genome sequencing datasets
2020
Overview
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. Competing Interest Statement The authors have declared no competing interest.
Publisher
Cold Spring Harbor Laboratory Press,Cold Spring Harbor Laboratory
Subject
