Computing Phylogenetic Informativeness

After you get the dependencies installed, computing the phylogenetic informativeness (PI) is rather easy. The typical invocation of the program looks like:

tapir_compute.py /your/input/nexus/ \
    /your/data/treefile.tree \
    --output /path/to/the/output \
    --times 1,2,3,4 \
    --intervals 1-5,5-10

This wil compute the PI from a folder of nexus files at /your/input/nexus/, against the tree that is located at /your/data/treefile.tree, for the the discrete times 1,2,3,4 and across the intervals (aka epochs) 1-5 and 5-10.

We describe each option (tapir_compute.py -h) in detail, below. We have separated these options into those pertinent to PI Computation Options and those for re-computation.

PI Computation Options

Positional arguments

alignments The folder of alignments

tree The input tree

Positional arguments are passed to the program by position. For example, to send the above to tapir_compute.py, you would type, on the command-line

tapir_compute.py alignments tree

Required arguments

We have several options that are requies, which can annoy some people. Here, we’ve made these options required because it makes the command-line invocation of the program less clumsy and more clear.

--times TIMES
	Comma-separated list of start times of interest (MYA)
--epochs EPOCHS
	Comma-separated list of epoch ranges of interest (MYA)

Optional arguments

These are true options in the sense that they are entirely optional - the defaults will be chose for you if you do not pass a value along with it’s corresponding option.

-h, --help
	show this help message and exit
--tree-format FORMAT
	The format of the tree (nexus or newick)
--output OUTPUT
	The path to the output directory
--hyphy HYPHY
	The path to hyphy (if not in $PATH)
--template TEMPLATE
	Path to the hypy temlate file if in non-standard location
--threshold THRESHOLD
	Minimum number of taxa without a gap for a site to be considered informative
--multiprocessing
	Enable parallel calculation of rates
--site-rates
	Use previously calculated site rates