Martin Hölzer1,2, Manja Marz1,2,3. 1. RNA Bioinformatics and High-Throughput Analysis, Faculty of Mathematics and Computer Science, Jena 07743, Germany. 2. European Virus Bioinformatics Center, Friedrich Schiller University Jena, Jena 07743, Germany. 3. FLI Leibniz Institute for Age Research, Marz Associated Research Group, Jena 07745, Germany.
Abstract
SUMMARY: PoSeiDon is an easy-to-use pipeline that helps researchers to find recombination events and sites under positive selection in protein-coding sequences. By entering homologous sequences, PoSeiDon builds an alignment, estimates a best-fitting substitution model and performs a recombination analysis followed by the construction of all corresponding phylogenies. Finally, significantly positive selected sites are detected according to different models for the full alignment and possible recombination fragments. The results of PoSeiDon are summarized in a user-friendly HTML page providing all intermediate results and the graphical representation of recombination events and positively selected sites. AVAILABILITY AND IMPLEMENTATION: PoSeiDon is freely available at https://github.com/hoelzer/poseidon. The pipeline is implemented in Nextflow with Docker support and processes the output of various tools.
SUMMARY: PoSeiDon is an easy-to-use pipeline that helps researchers to find recombination events and sites under positive selection in protein-coding sequences. By entering homologous sequences, PoSeiDon builds an alignment, estimates a best-fitting substitution model and performs a recombination analysis followed by the construction of all corresponding phylogenies. Finally, significantly positive selected sites are detected according to different models for the full alignment and possible recombination fragments. The results of PoSeiDon are summarized in a user-friendly HTML page providing all intermediate results and the graphical representation of recombination events and positively selected sites. AVAILABILITY AND IMPLEMENTATION: PoSeiDon is freely available at https://github.com/hoelzer/poseidon. The pipeline is implemented in Nextflow with Docker support and processes the output of various tools.
Authors: Franziska Hufsky; Kevin Lamkiewicz; Alexandre Almeida; Abdel Aouacheria; Cecilia Arighi; Alex Bateman; Jan Baumbach; Niko Beerenwinkel; Christian Brandt; Marco Cacciabue; Sara Chuguransky; Oliver Drechsel; Robert D Finn; Adrian Fritz; Stephan Fuchs; Georges Hattab; Anne-Christin Hauschild; Dominik Heider; Marie Hoffmann; Martin Hölzer; Stefan Hoops; Lars Kaderali; Ioanna Kalvari; Max von Kleist; Renó Kmiecinski; Denise Kühnert; Gorka Lasso; Pieter Libin; Markus List; Hannah F Löchel; Maria J Martin; Roman Martin; Julian Matschinske; Alice C McHardy; Pedro Mendes; Jaina Mistry; Vincent Navratil; Eric P Nawrocki; Áine Niamh O'Toole; Nancy Ontiveros-Palacios; Anton I Petrov; Guillermo Rangel-Pineros; Nicole Redaschi; Susanne Reimering; Knut Reinert; Alejandro Reyes; Lorna Richardson; David L Robertson; Sepideh Sadegh; Joshua B Singer; Kristof Theys; Chris Upton; Marius Welzel; Lowri Williams; Manja Marz Journal: Brief Bioinform Date: 2021-03-22 Impact factor: 11.622