This pipeline holds an automated method to analyze mitotype data for a tonsa based on the phylogeny of Figueroa et al., 2020: Phylogeography ofAcartia tonsaDana, 1849 (Calanoida: Copepoda)and phylogenetic reconstruction of the genusAcartiaDana, 1846.
View the help file with: ./mitotype_pipeline.sh --help or ./mitotype_pipeline.sh -h
This currently lives at: /data/copepods/mitotypes and should be executable by everyone in the lab. Let me know if there are issues.
To execute the pipeline, on dott run the following:
./mitotype_pipeline.sh your.fasta plot_name
where your.fasta contains your sequence data and plot_name is the name you want for your output plot.
All output will be directed to output/, which will be created if it doesn't already exist.
I assume some R packages are installed: treeio, tidyverse, ggtree, ape, stringr.
All of this could be run wherever, but paths to mr bayes and muscle are hard coded right now, so you'd need to edit that if exporting this elsewhere.