# Options

#### ./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).

OPTIONS:

- -I: inseparable pairs only will be computed (Identity matrix)
- -S: genealogically ordered pairs only will be computed (S matrix)
- -B: (both) inseparable pairs and genealogically ordered pairs will be computed (S+Id matrix) (default: -S option is used, genealogically ordered pairs only will be computed (S+Id matrix)
- -b: outputs branches number, length and associated probabilities
- -d: (distribution) output on stderr the inseparable pairs and/or genealogically ordered pairs probabilities distribution
- -m: (matrix) output on stderr the S or S+Id matrix
- -t: (tree) output the tree on stderr
- -e: (e1,e2) output on stderr the e1 and e2 vectors (of mutations)
- -v: (verbose) outputs running progression of the program
- -a: select all options b,d,m,t,e
- TREE_FILE: tree file in Newick tree format with events instead of bootstrap values (see the manual)
One or more options can be turned on; the description for each of them are also 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.