The pipeline for neutral mutation spectra evaluation based on evolutionary data

2 pipeline versions

1. NeMu pipeline including tblastn-head - input is single protein sequence that will be used by tblastn to search homologous nucleotide sequences in selected database. After this step NeMu-core executes with phylogeny and spectra inference
2. NeMu-core pipeline - input is multifasta of nucleotide sequences, that used for phylogeny and spectra inference

Config examples

1. Config for comparative species analysis - on many species

2. Config for intraspecies analysis - on single species

   • Don't forget to change process.container and singularity.runOptions parameters according to execution environment

Test

Run the script (from this directory) to test the pipeline on your computer. Don't forget to change path to singularity container and runOptions in the config file.

Important about runOptions: if you run the pipeline from disk that don't contain your $HOME directory, you must write in the runOptions --bind $MOUNT_PATH, where $MOUNT_PATH is the mount point of the disk from that you want to execute the pipeline (--bind /scratch in my case). If you run the pipeline from any subdirectory of your $HOME, delete this runOptions from config file.

bash test.sh