High Performance Computing course- Biological Applications- May 24, 2016
Your assignment: Generate a phylogenetic tree using MrBayes for whiteflies!
1) Download the slurm script and the DNA data files and put them in your /scratch on Magnus
2) Modify the slurm script to your account specifications.
3) Open the DNA data file in an editor and look at the MrBayes block
4) How many generations are we asking Magnus to complete?
5) Tell me what all the parameters in the MrBayes block are doing- you can use the manual to help.
6) Start a MrBayes run on Magnus. What command to you use to submit your script?
7) How long did it take?
8) Download Figtree and open your .con file. The .con file contains a consensus of all the trees.
9) Screenshot or save as a .pdf the .con file and submit this with your answers to the questions above.
10) 1 paragraph about what you liked about this assignment.
11) Email me (laura.boykin@uwa.edu.au) the answers to the above question (either in a word document or text editor) and also the image of the phylogenetic tree.
12) Due June 3, 2016
MrBayes manual: here
Files you need to start analyses on Magnus:
Slurm Script (4chains.mod.sh)
DNA data (whiteflydata.mrbayes)
| 4chains.sh |
| whiteflydata.mrbayes |
Slurm on Magnus:
Slurm information from Pawsey
To view the phylogeny (.con file)- use FigTree
Other Phylogenetics tutorials:
Bodega Bay
Tutorial to using MrBayes 3.2 (Bodega Bay)
Workshop on Molecular Evolution (in general)
Workshop on Molecular Evolution (software w/ many useful tutorials)
Slurm information from Pawsey
To view the phylogeny (.con file)- use FigTree
Other Phylogenetics tutorials:
Bodega Bay
Tutorial to using MrBayes 3.2 (Bodega Bay)
Workshop on Molecular Evolution (in general)
Workshop on Molecular Evolution (software w/ many useful tutorials)
