ArticleBMC bioinformatics2021
cognac: rapid generation of concatenated gene alignments for phylogenetic inference from large, bacterial whole genome sequencing datasets.
Article in BMC bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 19 citations in OpenAlex.
- Genomic inference of sites of transmission during regional spread of blaNature communications · 2026Article
- Buscogeny: A BUSCO leveraged phylogenomic tree builder.International microbiology : the official journal of the Spanish Society for Microbiology · 2026Article
- Genomic screening of eight antibiotic-resistant Pseudomonas isolated from rainbow trout (Oncorhynchus mykiss).Access microbiology · 2026Article
- Multi-host distribution of Rhodococcus equi (Prescottella equi) strains and their phylogenomic clustering.BMC microbiology · 2025Article
- Longitudinal genomic surveillance of carriage and transmission of Clostridioides difficile in an intensive care unit.Nature medicine · 2023Article
- Distinct Origins and Transmission Pathways ofJournal of clinical microbiology · 2023Article
- Phenotypic and Genomic Diversification in Complex Carbohydrate-Degrading Human Gut Bacteria.mSystems · 2022Article
- The survivor strain: isolation and characterization ofFrontiers in bioengineering and biotechnology · 2022Article
- Regional Spread of blaNDM-1-Containing Klebsiella pneumoniae ST147 in Post-Acute Care Facilities.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2021Article
- Genomic Update of Phenotypic Prediction Rule for Methicillin-Resistant Staphylococcus aureus (MRSA) USA300 Discloses Jail Transmission Networks with Increased Resistance.Microbiology spectrum · 2021Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
backgroundThe 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.
resultsWe 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.
conclusionsWe 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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