Code
Code Availability
We are in the process of migrating (and updating) all code to GitLab (https://gitlab.com/barker-lab). Bioinformatic tools from the Dlugosch lab previously available on evopipes.net are being migrated as well.
EvoPipes
A repository of the core EvoPipes pipelines is available at https://gitlab.com/barker-lab/EvoPipes. Included in this repository is an EvoPipes Docker that provides a fully functioning distribution of EvoPipes. It is recommended that most users run the Docker version.
MAPS: Multi-tAxon Paleopolyploid Search algorithm
Current version of the 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. Download now at https://gitlab.com/barker-lab/MAPS
Flow chart of the 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).
Animal Chromosome Count Database
The Animal Chromosome Count Database (ACC) is the largest database of animal chromosomal counts. We have curated chromosome numbers across the animal Tree of Life to make data accessible for people interested in understanding the potential links between biological processes and patterns to broad chromosomal changes in animals. Access the data and find out more here:
ACC Preprint: https://doi.org/10.1101/2020.10.10.334722
