EDEN: evolutionary dynamics within environments.
Ontology highlight
ABSTRACT: Summary
Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions. However, phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big data. EDEN is the first software for the rapid detection of protein families and regions under positive selection, as well as their associated biological processes, from meta- and pangenome data. It provides an interactive result visualization for detailed comparative analyses.Availability and implementation
EDEN is available as a Docker installation under the GPL 3.0 license, allowing its use on common operating systems, at http://www.github.com/hzi-bifo/eden.Contact
alice.mchardy@helmholtz-hzi.de.Supplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Munch PC
PROVIDER: S-EPMC5860032 | biostudies-literature | 2017 Oct
REPOSITORIES: biostudies-literature
Publications
EDEN: evolutionary dynamics within environments.
Münch Philipp C PC Stecher Bärbel B McHardy Alice C AC
Bioinformatics (Oxford, England) 20171001 20
<h4>Summary</h4>Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions. However, phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big dat ...[more]
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