getphylo: rapid and automatic generation of multi-locus phylogenetic trees

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Genomic data is rapidly increasing, necessitating efficient phylogenetic tree construction tools.
• Current methods often rely on extensive databases or lengthy de novo calculations, limiting speed and taxonomic scope.

Purpose of the Study:

• To introduce getphylo, a Python tool for rapid, de novo generation of genome-scale phylogenetic trees.
• To address limitations of existing tools regarding speed, database dependency, and taxonomic scope.

Main Methods:

• getphylo identifies orthologues heuristically by searching for single-copy genes across input genomes.
• Phylogeny is inferred using maximum likelihood from a concatenated alignment of all coding sequences.
• The tool was benchmarked against autoMLST and GTDB-tk using bacterial and eukaryotic genomes.

Main Results:

• getphylo produces phylogenetic trees of comparable quality to existing tools but in a fraction of the time.
• The tool demonstrated flexibility across diverse datasets, including bacterial and eukaryotic genomes and biosynthetic gene clusters.
• Benchmarking showed getphylo's superior speed without compromising tree quality.

Conclusions:

• getphylo is a fast, reliable, and automated tool for generating genome-scale phylogenetic trees.
• It eliminates the need for large local databases and intensive computation, making phylogenetics more accessible.
• The tool's speed, flexibility, and usability make it a valuable addition to the phylogenetics toolkit.