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New software automates and improves phylogenomics from next-generation sequencing data

To reconstruct phylogenetic trees from next-generation sequencing data using requires a time-consuming combination of bioinformatic procedures including genome assembly, gene prediction, orthology identification and multiple alignment. As a consequence, more recently, scientists have relied on a simpler method where short sequence reads from each species are aligned directly to the of a single reference sequence.

The authors, Bertels, et. al., in the advanced online edition of , not only show that this simpler method can lead to significant errors and biases in , but have also developed a new online tool called REALPHY (reference based phylogeny builder) that automatically reconstructs evolutionary trees from data generated by next-generation sequencing data in a way that avoids these errors and biases. Applying this new method to several collections of bacterial genomes, the authors show that the method is at least as accurate, and often more accurate, than traditional methods.

“We believe REALPHY will make it easy for any researcher to obtain accurate phylogenies from next-generation sequencing data,” said corresponding author of the University of Basel, Switzerland.

The software is simple enough for biologists without much bioinformatics expertise to use. REALPHY is available through a webserver, allowing for the fast and automated generation of multiple sequence alignments from a variety of genome sequence data formats (e.g., Illumina sequences, draft genomes, fully sequenced genomes), and the automated reconstruction of phylogenies from these alignments.


Molecular Biology and Evolution (Oxford University Press)