Code

EvoPipes.net

Our public server to run many of our pipelines and download code. It is currently down due to hardware failures. We are in the process of migrating (and updating) all code to our lab bitbucket (https://bitbucket.org/barkerlab/). Bioinformatic tools from the Dlugosch lab also available here and being migrated as well.

MAPS: Multi-tAxon Paleopolyploid Search algorithm

Current version of our MAPS (Li et al. 2015; Li et al. 2018) scripts and accompanying simulation code for identifying shared whole genome duplications across multi-species gene family phylogenies. Full description of algorithms and simulations coming soon in Li et al. (in prep).

Flow chart of our MAPS algorithm (Li et al. 2015) from Li et al. in preparation.
Sample of simulated WGDs used for training machine learning models of WGD inference in forthcoming tool SLEDGE (Sutherland et al. in prep).