HyDe-CNN: Hybridization detection with convolutional neural networks

Citation

Blischak, P. D., M. S. Barker, and R. N. Gutenkunst. 2020. Chromosome-scale inference of hybrid speciation and admixture with convolutional neural networks. bioRxiv doi:.

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Requirements

Below are the Python and R packages that were used for performing the analyses in our paper. We used Python v3.7 and R v3.6.

Python packages:

The environment.yml has all of the specifications needed to recreate the conda environment we used for simulating, training, and testing HyDe-CNN. If you just want to install the essential packages, they are listed below:

• numpy
• matplotlib
• tensorflow
• sklearn
• tskit
• msprime
• pysam

R packages:

• tidyverse
• abcrf
• caret
• patchwork