Phylogenetics: r8s Lab

	EEB 349: Phylogenetics
	The goals of this final lab are to learn how to: (1) set up a NEXUS file for the r8s program; (2) interpret the most important parts of the output of r8s; (4) view a tree with divergence times produced by r8s in TreeView.

Using r8s to estimate divergence times

There is no version of r8s for the Windows operating system, so we will use the version installed on the Bioinformatics cluster.

Start the program PuTTY and connect to bbcxsrv1.biotech.uconn.edu

There should be a shortcut to PuTTY on your desktop. Using PuTTY, connect to bbcxsrv1.biotech.uconn.edu.

alleyn [/home/tmp1/dist/src] 8% cd ../sample
alleyn [/home/tmp1/dist/sample] 9% ls
r8s SAMPLE_CONSTRAINTS SAMPLE_FLU SAMPLE_SIMPLE
SAMPLE_1.7 SAMPLE_CROSSVAL SAMPLE_LOCAL_CLOCK SAMPLE_SUPERTREE

Inspecting the SAMPLE_SIMPLE file Use the more command to see the first few lines of the SAMPLE_SIMPLE file. Note that r8s uses the NEXUS format for its input files:

alleyn [/home/tmp1/dist/sample] 10% more SAMPLE_SIMPLE
#NEXUS

[
** A sample data set illustrating use of divergence time estimators in r8s.
]

begin trees;

[
** The following branch lengths were obtained from PAUP using maximum likelihood
]

tree PAUP_9 = [&U] 
 (Marchantia:0.033817,(Lycopodium:0.040281,((Equisetum:0.048533,(Osmunda:0.033640,Asplenium:
0.036526):0.000425):0.011806,((((Cycas:0.009460,Zamia:0.018847):0.005021,Ginkgo:0.014702):1.687e-86,((Pinus:0.
   021500,(Podocarpac:0.015649,Taxus:0.021081):0.006473):0.002448,(Ephedra:0.029965,(Welwitsch:0.011298,Gnetum:0.
   014165):0.006883):0.016663):0.006309):0.010855,((Nymphaea:0.016835,(((((Saururus:0.019902,Chloranth:0.020151):
   1.687e-86,((Araceae:0.020003,(Palmae:0.006005,Oryza:0.031555):0.002933):0.007654,Acorus:0.038488):0.007844):1.
   777e-83,(Calycanth:0.013524,Lauraceae:0.035902):0.004656):1.687e-86,((Magnolia:0.015119,Drimys:0.010172):0.005
   117,(Ranunculus:0.029027,((Nelumbo:0.006180,Platanus:0.002347):0.003958,(Buxaceae:0.013294,((Pisum:0.035675,(F
   agus:0.009848,Carya:0.008236):0.001459):0.001994,(Ericaceae:0.019136,Solanaceae:0.041396):0.002619):1.687e-86)
   :0.004803):1.687e-86):0.006457):0.002918):0.007348,Austrobail:0.019265):1.687e-86):1.687e-86,Amborella:0.01926
   3):0.003527):0.021625):0.012469):0.019372);
End;

[** Beginning of the rates block containing commands for r8s **]

begin rates;

[* The next line is REQUIRED.]

blformat nsites=952 lengths=persite;

--More-- (43%)

You can see more of the file by pressing the spacebar, and you can quit viewing the file by pressing the letter q (for quit). Dissecting the data file See if you can answer these questions just by looking at the SAMPLE_SIMPLE file:

Which NEXUS blocks are present? (Hint: you should find 2 NEXUS blocks in this file)

Why does r8s need to know the number of sites? (as in the "blformat nsites =952 lengths=persite" command)

Below is the tree specified in the SAMPLE_SIMPLE file: