Ima3 REST

IMa3 interface: ima3_xsede

IMa3 Program
copyright by Jody Hey.

use toolid = IMA3_XSEDE

Command line options:

input.infile_ - The main input file. This is the same format as IMa2 and Ima2p.
input.specify_tifile1_ - Infile Select your first *.ti file; when $run_option0 = 1.
input.specify_tifile2_ - Infile Select your second *.ti file; when $run_option0 = 1.
input.specify_tifile3_ - Infile Select your thrid *.ti file; when $run_option0 = 1.
input.infile_specify_nestmod_ - Infile Name of file with nested models to be tested (LOAD-GENEALOGY mode only), invokes -c2
input.markovchainstate_file_ - Infile Select the .mcf file with saved Markov chain state generated in previous run (-f); when runtype=3
input.datatype5_file_ - Infile Select file with parameter priors; when $calc_option3 is selected.

User Configurable Parameters.

vparam.runtime_ (Float) Maximum Hours to Run (up to 168 hours)
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)

Set Burnin
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_gentime_ (Integer) Generation time in years (-u) - for use with -p3 (default is 1).
vparam.specify_stepscreen_ - Integer; Number of steps between screen output (MCMC mode only)

Run Options
vparam.run_option0_ Switch; Load genealogies from previous run(s) (-r0)
vparam.specify_tiname - String, Base name (no extension) of *.ti files with genealogy data when run_option0 = 1.
vparam.run_option1_ - Switch, Do not save genealogies to a file (-r1)
vparam.run_option2_ - Switch, Save the state of the Markov chain in a file (-r2)
vparam.run_option3_ - Switch, Start run by loading a previously saved *.mcf file (-r3)
vparam.run_option4_ - Swtich, Write all mutation related rates to stdout.txt (-r4)
vparam.run_option5_ - Switch, Print burntrend file at end of burnin period (-r5)
vparam.run_option6_ - Switch, When loading mcf files (-r3,-r7), use previous run as burnin (-r6)
vparam.run_option7_ - Switch, Load mcf if present, AND save to mcf (-r7)
vaparam.markovchainstate_filename_ - String, Enter the mcf file name (-f)
vparam.run_option8_ - Switch, Use unique IMburn/run files with outfilename as a prefix (-r8)
vparamspecify_numsteps_ Integer, Specify the number of steps between geneology saving (-d)

Calculation options:
vparam.calc_option0_ - Switch, Likelihood of data functions return a constant -posterior should equal prior (-c0)
vparam.calc_option1_ - Switch, Include ranges on mutation rates as priors on mutation rate scalars (-c1)
vparam.calc_option2_ Switch, Joint posterior density calculations, for LLR tests of nested models (-c2)
vparam.calc_option3_ Switch, Get prior distribution terms from file (-c3)

Heating Terms
vparam.specify_numchains_ - Integer, Number of chains, all models (-hn)
vparam.specify_firstheatparam_ - Float, Specify the first heating parameter (-ha; sigmoid or geometric)
vparam.specify_secondheatparam_ - Float - Specify the second heating parameter (-hb; geometric only)

Model Options
vparam.model_option0_ Switch Estimate population topology: 3 populations required (-j0)
vparam.specify_topologypr_ - Sting - Specify population topology prior (-x)
vparam.model_option1_ - Switch - Add a non-sampled ghost population to the model (-j1)
vparam.model_option2_ - Switch - Migration prior follows exponential distribution (-j2)
vparam.model_option3_ - Switch - Use hyperpriors specified by -q and -m (-j3)
vparam.model_option4_ - Switch - Migration only between sister populations (-j4)
vparam.model_option5_ - Switch - One migration parameter for each pair of populations (-j5)
vparam.model_option6_ - Switch - Migration only between sampled populations (-j6)
vparam.model_option7_ - Switch - Period specific parameters (-j7)
vparam.model_option8_ - Switch - No migration in the model (-j8)
vparam.model_option9_ - Switch - One single migration parameter for all pairs of populations (-j9)
vparam.model_optionx_ - Switch - One single population size parameter for all populations (-jx)
 
 Run duration options
vparam.specify_hours_ - Float - Time in hours of the sampling period (must have a decimal) (-l)
vparam.specify_runduration1_ - Float - Number of phylogenies to save:
vparam.specify_runduration2_ - Float - Number of times the topologies are sampled
vparam.specify_runduration2b_ - Float - Number of times the genealogies are sampled
vparam.specify_runduration3_ - Integer - Number of genealogies to load from file
 
Output options
vparam.output_option0_ - Switch Turn off trend plots in outfile (-p0)
vparam.output_option1_ - Switch Turn off plots of marginal curves in outfile (-p1)
vparam.output_option2_ - Switch Print TMRCA histogram for each genealogy  (-p2)
vparam.output_option3_ - Switch Print histogram of splitting times divided by prior (-p3)

vparam.specify_gentime_ - Integer - Generation time in years (-u for use with -p3; default is 1)
vparam.specify_mutratescalar_ - Integer - Mutation rate scalar for relevant loci -for use with -p3 (-y)

vparam.output_option4_ - Switch - Turn off printing estimates and histograms of population migration rate (-p4)
vparam.output_option5_ - Switch - Print pairwise probabilities that one parameter is greater than another (-p5)
vparam.output_option6_ - Switch - Print histograms of the number of migration events (-p6)
vparam.output_option7_ - Switch - Print joint estimate for splitting times (-p7)

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