A simple application to interrogate the molecular evolution of a single gene
This application is currently designed to run in an HPC environment.
There is an assumption that the freely available Anaconda software is installed on your machine.
You will also need to download the standalone hyphy-analyses repository (https://github.com/veg/hyphy-analyses). Make sure to modify the config.yaml to point to the correct directory on your system
git clone https://github.com/aglucaci/GeneInvestigator.gitconda env create -f environment.yaml. This will create a virtual environment called (GeneInvestigator) with the necessary dependencies.- At this point, run
conda activate GeneInvestigatorand your environment will be ready to go.
For example, if we are interested in the TP53 gene: https://www.ncbi.nlm.nih.gov/gene/7157/ortholog/?scope=117570&term=TP53
Download all information: Tabular data, RefSeq Transcripts, and RefSeq Protein. (Typically one gene per species, but all transcripts per species is also available)
The following are JSON files produced by HyPhy analyses. These can be visualized by the appropriate module from HyPhy Vision (http://vision.hyphy.org/). Analysis file names contain the method used (SLAC, FEL, PRIME, FADE, MEME, CFEL, etc), and if appropriate -- the set of branches to which the analysis was applied.
── results/TP53
│ ├── TP53.FEL.json
│ ├── TP53.FUBAR.json
│ ├── TP53.BUSTEDS.json
│ ├── TP53.MEME.json
│ ├── TP53.ABSREL.json
│ ├── TP53.SLAC.json
│ ├── TP53.BGM.json
│ ├── TP53.PRIME.json
│ ├── TP53.FMM.json
│ ├── TP53.ABSREL-MH.json
│ ├── TP53.BUSTEDS-MH.json
│ ├── TP53.MSS.json
│ ├── TP53.BUSTEDS-MSS.json
Alternative name: Analysis of Orthologous Collections (AOC)