Code

 

Code Availability

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 previously available on evopipes.net are being migrated as well. Please keep a look out for a refresh of the evopipes.net suite of tools this year, including downloadable and containerized versions of the pipelines! Read more about the current tool collection here: https://doi.org/10.4137%2FEBO.S5861

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MAPS: Multi-tAxon Paleopolyploid Search algorithm

Current version of our MAPS (Li et al. 2015Li et al. 2018) scripts and accompanying simulation code for identifying shared whole genome duplications across multi-species gene family phylogenies. Full description of algorithms, simulations, and performance coming soon in Li et al. (in prep). Download now at https://bitbucket.org/barkerlab/maps

Flow chart of our MAPS algorithm ( Li et al. 2015 ) from Li et al. in preparation.

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).

Sample of simulated WGDs used for training machine learning models of WGD inference in forthcoming tool SLEDGE (Sutherland et al. in prep).