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Parallelization at the different stages of the pipeline is achieved using the Python implementation of the message passing interface (MPI for Python (Mpi4Py) [33]).
All genomic analyses were conducted using the Python implementation.
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For the multi-locus mixed model (MLMM) analysis (Segura et al. 2012), we used the Python implementation (https://github.com/bvilhjal/mixmogam, version 1.0) with minor modifications to support our data formats.
Random Forest was implemented using the Python package scikit-learn.
DNNs were implemented using the Python library Tensorflow [35].
Macau was implemented using the Python package Macau.
Python scripts can also be written and executed within MorphoGraphX using the Python Script process.
It is written using the Python programming language.
All figures were produced using the Python module Matplotlib [ 72].
For this work, therefore, we used the Python standard implementation of SVD from the NUMPY library and its dependencies.
In "differential" mode enrichment signals are windowed and corrected for sequencing-depth (i.e., normalized) using the provided Python implementation of the DESeq algorithm [ 42].
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