The TrEase web service: inferring phylogenetic trees with ease

Abstract

Phylogenetic inference is done regularly in many biological studies not focussed on the phylogeny itself, but which use phylogeny as a tool to infer hypotheses for the interpretation of laboratory experiments. However, phylogenetic inference is often performed at low standards in these studies, which can result in wrong interpretations. Using high-standard phylogenetic inference tools usually requires substantial methodological knowledge or is only possible with paid tools. To enable beginners, researchers for which phylogeny is just one tool of many, and scientists in biodiversity discovery a quick and easy access to current phylogenetic methods, the TrEase web service with an intuitive interface was developed. It offers a complete pipeline with commonly used phylogeny-related software, which can run the whole process of sequence acquisition, reference sequence search, alignment and phylogenetic inference with a single execution command once the necessary parameters have been selected from drop-down menus. It allows choosing alternate programmes for each step and also offers the flexibility to use any part of the pipeline independently. Along with providing a compact pipeline, this web service provides several functionalities to avoid manual intervention such as sorting sequences into the same orientation, cutting reference sequences, removal of redundant sequences and the possibility to choose reference sequences from top ‘species’ hits instead of top GenBank entry hits. All resulting trees and intermediate files are made available for download for subsequent use. Thus, the TrEase service offers a barrier-free entry into standard phylogenetic analyses. It is available at http://thines-lab.senckenberg.de/trease.