https://github.com/trvrb/PACT
Revision 42123addebd72d7361f7b2cef658a0f8e5dc95dd authored by Trevor Bedford on 22 April 2014, 02:50:27 UTC, committed by Trevor Bedford on 22 April 2014, 02:50:27 UTC
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Tip revision: 42123addebd72d7361f7b2cef658a0f8e5dc95dd authored by Trevor Bedford on 22 April 2014, 02:50:27 UTC
Fix string import.
Fix string import.
Tip revision: 42123ad
README.md
The program PACT computes a variety of statistics from a sample of genealogical trees. It is meant
to extend the functionality of already existing coalescent inference programs such as Migrate,
BEAST, IM and LAMARC. PACT reads genealogies in NEWICK format and performs various operations on
these genealogies. PACT is designed to work with both structured genealogies and also with
genealogies assembled from temporally spaced sequence data.
The functionality of PACT is highly modular, relying on combinations of tree manipulation operations
and summary statistics to produce useful results. For example, the operation tmrca returns the TMRCA
of the entire tree, but when combined with the prune to label, it returns the TMRCA of samples with
a specified label. In another example, diversity at a specified point in time may be calculated with
a combination of time slice and diversity.
On UNIX systems you can compile with:
make
PACT requires two files to run:
in.param (parameter listing)
in.trees (NEWICK trees)
Available parameters can be found in parameters.txt. Full documentation can be found in
[`pact_manual.pdf`](pact_manual.pdf).
Copyright 2011 Trevor Bedford. Distributed under the GPL v3.
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