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Hägglund E, Andersson SGE, Guy L
Bioinformatics 39 (12) - [2023-12-01; online 2023-12-07]
The profusion of sequenced genomes across the bacterial and archeal domains offers unprecedented possibilities for phylogenetic and comparative genomic analyses. In general, phylogenetic reconstruction is improved by the use of more data. However, including all available data is (i) not computationally tractable, and (ii) prone to biases, as the abundance of genomes is very unequally distributed over the biological diversity. Thus, in most cases, subsampling taxa to build a phylogeny is necessary. Currently, though, there is no available software to perform that handily. Here we present TADA, a taxonomic-aware dataset selection workflow that allows sampling across user-defined portions of the prokaryotic diversity with variable granularity, while setting constraints on genome quality and balance between branches. TADA is implemented as a snakemake workflow and is freely available at https://github.com/emilhaegglund/TADA.
PubMed 38060257
DOI 10.1093/bioinformatics/btad742
Crossref 10.1093/bioinformatics/btad742
pmc: PMC10733731
pii: 7461186