Dear community
I need to set up a software pipeline to detect signatures of selection between two mouse populations; one has been selected for traitX over the past 4 decades and the other has not been selected and is considered as a control population. Both differ significantly for the trait of interest. The starting data will come from DNA sequencing.
My former background is not in population genetics, so I am looking for guidance on which softwares to install in a high performance cluster, and to learn how they work and why they apply to my data.
Searching in the literature I found a paper from 2014 that precisely adresses my issue, including a training data set, which is perfect. However, it is almost 4 years old:
Cadzow, Murray, et al. "A bioinformatics workflow for detecting signatures of selection in genomic data." Frontiers in genetics 5 (2014).
My question to you is if the softwares mentioned in the pipeline (table 1) are still current, and if you have alternatives.
My aim is to set up and run the workflow to get a better feeling of the analysis, but since it will take a few days, I want to make sure that I am aiming in the right direction that allows me to learn as much as possible.
Thanks in advance!
