PhyTime on OpenStack - cdoorenweerd/PhylOStack GitHub Wiki

This HOWTO explains how to use PhyTime for a divergence time analysis on OpenStack with Ubuntu 14.04 LTS. For more information, see PhyML Github

Note: This HOWTO assumes you have installed PhyTime, which comes with the PhyML package that is installed through the BEAST_beagle_phyml script using the PhylOStack instructions and know how to connect via SSH, transfer files and use screen sessions.

Preparing input data

To run PhyTime three input files are required:

  1. A rooted tree in newick format, named RAxML_besttree_rooted.tre in the examples.
  2. The alignment with taxa that corresponds to the tree, in Phylip format, named alignment.phy.
  3. A text file with calibrations for nodes, named calibrations.txt, see example below

calibrations.txt

In this file the calibrations for the nodes are specified, in millions of years. Only normal distributions can be applied, by indicating the 5% and 95% boundaries. The age estimate for the root must always be indicated. A row indicates a clade, which can include multiple taxa. For more details refer to the PhyML manual.

taxonA taxonB taxonC    |   -25 -45
taxonD taxonE   |   -56 -80
@root@  |   -100 -130

Running PhyTime

Place the input files in a folder and copy this folder to the instance. SSH into the instance, navigate to the folder, start a Screen session (if desired) and run PhyTime with:

phytime -i alignment.phy -u RAxML_besttree_rooted.tre --calibration=calibrations.txt -m GTR -c 8 > STDOUT.phytime.log

-c 8 indicates that 8 different classes of rates in the Gamma distribution will be tested.

Results

  1. The intermediate results can be followed with the tail command on the STDOUT.phytime.log file. The first row shows the generation, which will go up to 1E6 by default. The numbers between brackets indicate ESS values.
  2. There will be a .stats file, which can be opened with Tracer to view all ESS values
  3. There will be a .trees file, which can be processed using TreeAnnotator using the command similarly to how it would be used with BEAST output:
treeannotator -heights mean -burnin 20 treesfile.trees finaltree.tre

The finaltree.tre can be opened with FigTree and will include error bars like BEAST output would.

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