PhyDGET is a method for analyzing transcriptome-wide expression data in a phylogenetic context to highlight genes whose expression is changing on particular branches of a phylogeny. PhyDGET is a Pythone3-based parallelized program that connects differential gene expression data transformation to Phylogenetic Comparative Methods (BayesTraits). PhyDGET also includes post-analysis tools for interpreting the results.
For complete details, see the manual for PhyDGET:
https://github.com/peaselab/PhyDGET/blob/main/phydget.pdf
or
https://github.com/peaselab/PhyDGET/blob/main/phydget.html
Link to publication: Layered evolution of gene expression in “superfast” muscles for courtship Pease JB*, Driver RJ*, de la Cerda DA, Day LB, Lindsay WR, Schlinger BA, Schuppe ER, Balakrishnan CN, Fuxjager MJ. 2022. Proceedings of the National Academy of the USA 119(14) e2119671119.
https://www.pnas.org/doi/10.1073/pnas.2119671119
Please also include the URL (https://www.github.com/peaselab/phydget).
Be sure also to cite BayesTrait.
- James B. Pease - www.peaselab.org
- David de la Cerda
This file is part of 'phydget'
'phydget' is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
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