PUmPER: phylogenies updated perpetually.
CONCLUSIONS
New sequence data useful for phylogenetic and evolutionary analyses continues to be added to public databases. The construction of multiple sequence alignments and inference of huge phylogenies comprising large taxonomic groups are expensive tasks, both in terms of man hours and computational resources. Therefore, maintaining comprehensive phylogenies, based on representative and up-to-date molecular sequences, is challenging. PUmPER is a framework that can perpetually construct multi-gene alignments (with PHLAWD) and phylogenetic trees (with ExaML or RAxML-Light) for a given NCBI taxonomic group. When sufficient numbers of new gene sequences for the selected taxonomic group have accumulated in GenBank, PUmPER automatically extends the alignment and infers extended phylogenetic trees by using previously inferred smaller trees as starting topologies. Using our framework, large phylogenetic trees can be perpetually updated without human intervention. Importantly, resulting phylogenies are not statistically significantly worse than trees inferred from scratch.


METHODS
PUmPER can run in stand-alone mode on a single server, or offload the computationally expensive phylogenetic searches to a parallel computing cluster. Source code, documentation, and tutorials are available at https://github.com/fizquierdo/perpetually-updated-trees.


BACKGROUND
Fernando.Izquierdo@h-its.org


BACKGROUND
Supplementary Material is available at Bioinformatics online.
Scientific Computing Group, Heidelberg Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Baden-Württemberg, Germany, Texas Advanced Computing Center, University of Texas, Austin, TX, 78758, USA, University of Michigan, Ann Arbor Department of Ecology and Evolutionary Biology, 48109, MI, USA and Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Postfach 6980, 76128 Karlsruhe, Baden-Württemberg, Germany.
Fernando
F
Izquierdo-Carrasco
John
J
Cazes
Stephen A
SA
Smith
Alexandros
A
Stamatakis
D030541:Databases, Genetic; D019669:Embryophyta / Q000235:genetics; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*; D012984:Software