IMA2_XSEDE IMa2 Program copyright 2011 by Jody Hey, Rasmus Nielsen, Sang Chul Choi, Vitor Sousa and Janeen Pisciotta command line this example: IMa2 -i infile.data -o IMa2_out.txt -b 50000 -L 100000 -d 100000 -m 1 -hfl -hn2 -ha0.999 -hb0.3 -p 2345678 -q 1 -s 3215 -t 3 input.infile_ - The main input file. input.infile_specify_nestmod_ - Name of file with nested models to be tested (LOAD-GENEALOGY mode only), invokes -c2 (-w) input.markovchainstate_file_ : infile Select the .mcf file with saved Markov chain state generated in previous run (-f); when runtype=3 vparam.runtime_ (Float) Maximum Hours to Run (up to 168 hours) vparam.choose_runmethod_ (Excl) Run duration (-l) in: 1. Number of genealogies to save. 2. Time in hours between outputs. vparam.specify_genealogies_ (Integer) Specify the number of genealogies to save (-l integer) vparam.specify_readgenealogies_ (Integer) Specify the number of genealogies to read from file only when a file is used. (-l integer) vparam.specify_hours_ (Float) Hours between writing of burntrend file ( - l) vparam.migration_prior_ (Float) Migration prior value (-m, maximum for uniform, mean if exponential distribution is used) vparam.outfile_name_ (String) Output file name (-o) vparam.max_popsize_ (Integer) Maximum for population size parameters (-q, 4Nu) vparam.specify_seed_ (Integer) Random number seed (-s default is taken from current time) vparam.specify_popsplit_ (Integer) Maximum time of population splitting (-t) vparam.specify_tiname_ (String) Base name (no extension) of *.ti files with genealogy data. vparam.specify_mutratescalar_ (Integer) Mutation rate scalar for relevant loci -for use with -p3 (-y) vparam.specify_runtype_ (Excl) Specify the run type (-r); 0. Load genealogies from previous run(s) 1. Do not save genealogies to a file 2. Save the state of the Markov chain in a file 3. Start run by loading a previously saved *.mcf file 4. Write all mutation related updates rates to stdout 5. Print burntrend file at end of burnin period. vparam.specify_calcoption_ (Excl) Specify the calculation option (-c) (when specify_runtype=2). 0; Likelihood of data functions return a constant; 1. Include ranges on mutation rates as priors; 2. Joint posterior density calculations; 3. Get prior distribution terms from file vparam.choose_burninsteps_ (Excl) Burn duration (-b) is in: 1. Number of Burnin Steps. 2. Time in hours between writing to burntrend. vparam.specify_burninsteps_ (Integer) Specify the number of burnin steps (-b) vparam.specify_burntrend_ (Float) Hours between writing of burntrend file (-b float; there must be a decimal). vparam.specify_numsteps_ - (Integer) - Specify the number of steps between geneology saving (-d) vparam.specify_modeloptions_ - (Excl) -Specify the model (-j) 1 Migration only between sister populations 2 One migration parameter for each pair of populations 3 Migration only between sampled populations 4 Add a non-sampled ghost population to the model 5 Separate population size and migration parameters in each period 6 No migration in the model 7 Migration prior follows exponential distribution with mean given by -m or in parameter prior file 8 Each ancestral population size is assumed to identical to that of their largest descendant population 9 One single migration parameter for all pairs of populations vparam.specify_gentime_ (Integer) Generation time in years (-u) - for use with -p3 (default is 1). Heating Terms vparam.specify_heatingmodel_ (Excl) Specify the heating model (-hf) g or l vparam.specify_numchains_ (Integer) Number of chains (-hn) vparam.specify_swapchains_ (Integer) Number of swap chains (-hk) vparam.specify_firstheatparam_ (Float) Specify the first heating parameter (-ha) vparam.specify_secondheatparam_ (Float) - Specify the second heating parameter (-hb) Output parameters vparam.specify_output_ (Integer) Specify the output type (-p); 1-8, 0 Turn off trend plots in outfile (default is to print trend plots) 1 Turn off plots of marginal curves in outfile (default is to print marginal density plots) 2 Print TMRCA histogram for each genealogy (MCMC mode only) 3 Print histogram of parameters on demographic scales (requires mutation rate(s) in data file) 4 Print histogram of splitting times divided by prior (do not use with -j0 or when only 2 sampled populations 5 Print estimates and histograms of population migration rate (2NM) 6 Print pairwise probabilities that one parameter is greater than another 7 Print histograms of the number of migration events (MCMC mode only) 8 Print joint estimate for splitting times (MCMC mode only, for models with 3, 4 or 5 populations)