MCB 5472 : Inferring Phylogenies #1

Please send your answers per email to, or hand in a hardcopy

Please let me know, how far you got during the lab. If most students didn't finish, we may continue this next week!


1) ML on protein sequences using PhyML on the cluster

a) For a dataset of your choice (aligned amino acid or nucleotide sequences) use PhyML (enter "phyml" at the command line) and calculate the tree with the highest likelihood using a model for Among Site Rate Variation (ASRV) that has a proportion of invariant site estimated from the data, and that describes the remaining sites with 4 rate categories that are a discrete approximation of a continuous Gamma distribution whose shape parameter is estimated from the data.

If you do not have a dataset, you can use atp_all.phy

2) Using the same dataset and the same model in TREE-PUZZLE

Invoke TREE-PUZZLE from the command line by typing "puzzle"

Use the tree from (3) as usertree (option k). Take you time in selecting the correct model ! (four rate categories plus invariant sites).


2B) Strict Molecular Clock

Repeat the analyses from above, but estimate if a strict molecular clock is compatible with the data (option z).

Select the pinvar and alpha from the previous analysis.

For a large data set, this might take some time (about 20 minutes for archaea_euk.phy). Start it, once it is running, open a new ssh connection , and qlogin to a different node (preferred), alternatively you can send the process (running puzzle) into background. For the latter, stop the process in foreground by pressing down <ctrl> and <z> simultaneously. Then restart the process in background by typing
bg %1

While waiting, continue with your student project.


3) Puzzleboot (only if you have time, and you want to try this).

puzzleboot is a UNIX shell-script program that allows the distance matrix option of PUZZLE to be used in the context of a bootstrap analysis with PHYLIP programs (something which PUZZLE was not originally designed to do).

Use a file of your choice (needs to be phylip formatted).

Create 100 bootstrap samples using seqboot.

Copy and puzzle.cmds into the directory where you want to run the script. .
CAREFUL: puzzleboot removes all outfiles and outtrees from the directory it runs in!

change permission of
chmod u+x

Change the responses in puzzle.cmds to that they correspond to the model you want to use. You probably want to fix pinvar and alpha to values you already estimated! (if you don't, the program spends a long time to find ml estimates for these parameters)

Hint: to help trouble shooting, run the puzzleboot first on the original data (one file), move to the bootstrap sample only after you are happy with the commands file.

Run seqboot on your data. To execute the script type:

The output consists of 100 distance matrices, run them through neighbor or fitch. You need to select the m option.

You get the support values with consense.

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Work on your student project !