PUmPER: phylogenies updated perpetually.

SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: 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. CONTACT: Fernando.Izquierdo@h-its.org SUPPLEMENTARY INFORMATION: Supplementary Material is available at Bioinformatics online.

The iPlant Collaborative: Cyberinfrastructure for Plant Biology.

The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services.