cognac: rapid generation of concatenated gene alignments for phylogenetic inference from large, bacterial whole genome sequencing datasets

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 ana...

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Published in:BMC bioinformatics 2021-02, Vol.22 (1), p.70-70, Article 70
Main Authors: Crawford, Ryan D, Snitkin, Evan S
Format: Article
Language:English
Subjects:
Amino acids
Analysis
Bacteria
Bacteria - classification
Bacteria - genetics
Bacterial genetics
Biology
Concatenated gene tree
Core genome
Databases, Genetic
Datasets
Family Characteristics
Gene sequencing
Genes
Genome, Bacterial
Genomes
Multiple sequence alignment
Phylogenetics
Phylogeny
Prokaryotes
Software
Trees
Whole Genome Sequencing
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Snitkin, Evan S
description 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. 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. 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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subjects Amino acids
Analysis
Bacteria
Bacteria - classification
Bacteria - genetics
Bacterial genetics
Biology
Concatenated gene tree
Core genome
Databases, Genetic
Datasets
Family Characteristics
Gene sequencing
Genes
Genome, Bacterial
Genomes
Multiple sequence alignment
Phylogenetics
Phylogeny
Prokaryotes
Software
Trees
Whole Genome Sequencing
title cognac: rapid generation of concatenated gene alignments for phylogenetic inference from large, bacterial whole genome sequencing datasets
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