Positive Selection Detection and Recombination Analysis
Here we present PoSeiDon, a pipeline to detect significant positively selected sites and possible recombination events in an alignment of multiple coding sequences (Manual). Sites that undergo positive selection can give you insights in the evolutionary history of your sequences, for example showing you important mutation hot spots, accumulated as results of virus-host arms races during evolution.
PoSeiDon is easy to use: just provide your nucleotide coding sequences as one multiple FASTA file. After submission of your job, PoSeiDon will assign a unique ID that can be used to access all data when calculations are finished. If an email was provided, the results will be also send via mail. You can also provide optional information like one or multiple species as Outgroup (for tree drawing) and a name of a Reference species (amino acids of positive selected sites will be shown in relation to this species).
Example input file(partial Mx1 gene of bats, runs ~10 min)
Example output 1(Mx1 gene of bats, with insignificant recombination events)
Example output 2(p19 gene of Tombusvirus, no recombination detected)
Example output 3(Mx1 gene of rodents, recombination detected)
Check out our PoSeiDon Poster presented at the 27th Annual Meeting of the Society for Virology, Marburg, 2017.
If you use PoSeiDon please cite (publication in progress):
Hölzer M, Marz M. PoSeiDon: a web server for the detection of evolutionary recombination events and positive selection.
Computational power: The web server is running on a huge HPC cluster called ARA. This cluster was just build up in November 2016 and consists of a shared tier-3 high performance cluster (HPC) with a 260 TB infiniband storage and 128 nodes with 72 CPU cores each (2 x Intel Xeon “Scalable” 6140 18 Core 2,3 Ghz) and 192 GB RAM. Each PoSeiDon job is running on a single node and 72 cores.
- 22/05/2018, Version 1.2
- Adapted PoSeiDon to run in the new hardware environment of the ARA cluster
- 01/12/2017, Version 1.2
- Added mouse-over tool-tips to the output of PoSeiDon to increase user-friendliness
- Added a link to the online help to the PoSeiDon output
- 28/02/2017, Version 1.1
- New results page for recombination events
- New results page for parameter settings and executed commands
- New results page summarizing CodeML parameters and results
- Pimped the main output page (mouseover functionality, direct access to LRT results)
- Introduced a new null model M8a (Swanson et al. 2003)
- 23/11/2016, Version 1.0
- Initial PoSeiDon setup