EpiCs

Description


EpiCs (Evolutionary processes independence Computed statistics) calculates the p-value of the co-repartition of the occurrences of a pair of events on a phylogenetic tree under a model of independence. Taking into account the topology of the tree and the location of the occurrences of each events on this tree, the algorithm calculates an exact p-value, under a model of independence, of the co-repartition of those occurrences on the tree.

Usage


EpiCs is an open-source implementation of the algorithm written in C language. The best way is to download the distribution directory (epics-dist.tgz), to uncompress and unarchive it (with "tar xvzf epics_src.tgz" in a terminal), to go into the directory ("cd epics-dist") and to compile it (by typing "make"). This results in an executable named "epics". Thus EpiCs is run as a command line program. To run EpiCs, simply type:

./epics [OPTIONS]... < TREE_FILE

or

./epics [OPTIONS]... TREE_FILE

Only one input file (TREE_FILE) is needed, the input format (described in the user guide) is the same for any number of events.

./epics -h

will list all available options (h for help).

One or more options can be turned on; the description for each of them are available in the manual (which is included also in the tgz archive), and the options are also briefly explained when entering "./epics -h".

NOTE: if a pair of events (e1, e2) is given, epics will compute statistics for both orders, i.e. epics will test e1 against e2 and will compute statistics on all possible events with same number of mutations as e2, and reciprocally, it will test e2 against e1 and compute statistics on all possible events with same number of mutations as e1. For more than two events, all pairs of events will be tested also in both orders.

You can also download binaries for Linux and Macintosh.


[ICO]NameLast modifiedDescription
[   ]User guide25-Sept-2015 
[TXT]EpiCs distribution25-Sept-2015 
[TXT]EpiCs macintosh binary25-Sept-2015 
[TXT]EpiCs linux binary25-Sept-2015 

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