IMa3 Analysis

Wrapper for IMa3 executable. This wrapper will handle locating the proper version of IMa3 for the desired run, as well as providing multi-threading support if the system has the mpirun utility and the IMa executable was compiled with it. Most options for IMa3 are described in the IMa3 manual, and it is HIGHLY recommended that users overview this document before calling IMa3. Note that wrapper functions (--threads,--ima-path) require two dashes, while IMa arguments use only one.

Input Arguments

-i <input_file>
Name of IMa3 input file generated by PPP
-o <output_file>
Name of IMa3 output file. Additional files will use this as prefix.

Parameter Arguments

-q <max_pop_size>
Sets maximum population size parameter for all populations.
-m <migration_rate>
Sets migration rate prior.
-t <max_split_time>
Sets maximum splitting time parameter.

Wrapper Arguments

--threads <thread_count>
Set number of threads to use. This will check that the proper version of IMa3 has been compiled and the system has mpirun installed.
--ima-path <path_to_ima>
Path to IMa executable to use if not on system path. This should include the name of the executable, not just the path to it.