The scripts in this repository were written during the preparation of the following manuscript:
Divergent genes in gerbils: prevalence, relation to GC-biased substitution, and phenotypic relevance.
Yichen Dai, Rodrigo Pracana and Peter WH Holland
BMC Evol Biol 20, 134 (2020). https://doi.org/10.1186/s12862-020-01696-3
In this manuscript, we analysed the divergence between the protein-coding genes of two gerbil species and those of other rodents and of H. sapiens.
This repository is divided into three parts:
- Scripts used to find groups of orthologous genes between rodents and H. sapiens
- Scripts used to align each group of orthologous genes and to measure substitution rates from the resulting alignments
- Scripts used to measure protein dissimilarity between species for each group of orthologous genes
We used several conda environments in our analyses. All environments are listed in the software directory. We used the biobase environment as default, and the r environment for any in-line R code.
Shield:
This work is licensed under a Creative Commons Attribution 4.0 International License.
