Shell scripts and R code to accompany the paper

Cryptic diversity masks ecologically divergent coral species on tropical reefs

• Host mitochondrial genome assembly
• Host mitochondrial haplotype network
• Symbiont mitochondrial haplotype network
• Sequencing coverage summary

• Population Structure
• Phylogenetic inference from Mitochondrial genomes
• Demographic History with MSMC

All of the sections above are provided as processed markdown files. Clicking the link should display a web readable page with text, a few select commands and plots and tables. The code used to generate these pages is provided in the corresponding .Rmd file. If you would like to run the code in these files yourself you will need to;

1. Checkout this repository

git clone https://github.com/iracooke/pachysers_wgs.git

2. Download additional data not hosted on github due to size constraints

cd pachyseris_wgs
wget 'http://data.qld.edu.au/public/Q5999/iracooke/pachyseris_wgs/data.tgz' -O data.tgz
tar -zxvf data.tgz 

3. Open the project file in RStudio and open the desired file (eg 01_mitogenomes.Rmd). After installing any required R packages the code should run and produce plots and tables identical to those shown in the web links above.