All done in EVE cluster
We’ve looked at 3 methods for looking at population structure. We can also confirm this information on population structure from a phylogeny, by looking at how the individuals and populations cluster within a tree. More interestingly we can look at the relationships between populations (something that is not particularly clear with Admixture, sNMF and DAPC analyses)
For this exercise we will use RAxML on the EVE cluster to investigate phylogenetic relationships. Note that we will not do any phylogenetic dating here, for that you could use a variety of other things, for example BEAST.
#This is all done in the EVE cluster, it will take some time - we can reduce the number of bootstrap replicates to 5. You can build your own script or use the supplied one that you can edit (07_RAxML.sh)
#!/bin/bash
#SBATCH --job-name=RAxML
#SBATCH --mail-user=christopher_david.barratt@uni-leipzig.de
#SBATCH --mail-type=BEGIN,END,FAIL,TIME_LIMIT
#SBATCH --output=/work/$USER/ddRAD-seq_workshop/job_logs/%x-%j.log
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=40G
#SBATCH --time=12:00:00
#load environment
module purge
module load Anaconda3
source activate /global/apps/raxml_8.2.9
cd /work/$USER/ddRAD-seq_workshop/data/Exercises_4-8/RAxML/
# 10 bootstraps
raxmlHPC -f a -m GTRCAT -p 12345 -x 12345 -# 5 -s /work/$USER/ddRAD-seq_workshop/data/Exercises_4-8/RAxML/Lflav.phy asccorr=lewis -n bootstrapped
raxmlHPC -m GTRCAT -p 12345 -f b -t RAxML_bestTree.bootstrapped -z RAxML_bootstrap.bootstrapped -n FINAL_bootstrapped.tre
# move output files to outputs directory
mv /work/$USER/ddRAD-seq_workshop/data/Exercises_4-8/RAxML/RAxML*.* /work/$USER/ddRAD-seq_workshop/outputs/Exercise_7/
First we can run rsync again to pull in the files from RAxML into our desktop directory:
# transfer from the cluster
rsync -avhP -e 'ssh -p 8022' \
barratt@localhost:/work/$USER/ddRAD-seq_workshop/outputs/ \
/Users/cb76kecu/Desktop
Then…
Download and install Figtree on your computer.
Rsync the files from the EVE cluster back to your own computer again
Open Figtree and open the “RAxML_bipartitions.FINAL_bootstrapped.tre” file
A window will come up, just click ok (it’s about how to visualise the bootstrap values on nodes)
Your tree will appear, let’s visualise it better…
Open the “Trees” panel on the left, tick the “Root tree” box and then select “Rooting: Midpoint”
Go to the main menu and say “File > Import Annotations”. When the dialog box opens select the ddRAD-seq_workshop/data/Exercises_4-8/RAxML/RAD_IDs.txt file
Go back to Figtree and then open the “Tip Labels” panel, select “Display: NEW NAME”
You’ll see that the tip labels have now been replaced and you can compare them easily with the Admixture, sNMF and DAPC results
You can rerun RAxML with different parameter settings, for example by changing the number of bootstraps by changing the number in the first line to -# 10 instead of -# 5 (100 recommended for a full analysis, but this takes time). You could also look at different models of evolution instead of GTRCAT, or try a different ascertainment bias correction (not lewis)