scrm - An accurate coalescent simulator for genome-scale sequences

scrmisacoalescentsimulatorforbiologicalsequences.Differenttosimilar  programs,  it  can
       approximate  the  Ancestral  Recombination  Graph  with  arbitrary  precision. This allows you to rapidly
       simulate long sequences with essentially correct genetic linkage between sites.

Fiveindependentsitesfor10individualsusingKingman'sCoalescent:
              scrm 10 5 -t 10

   Asequenceof10kbfrom4individualsundertheexactARG:
              scrm 4 1 -t 10 -r 4 10000

   Asequenceof100MbusingtheSMC'approximation:
              scrm 4 1 -t 10 -r 4000 100000000 -l 0

   Sameasabove,butwithessentiallycorrectlinkage:
              scrm 4 1 -t 10 -r 4000 100000000 -l 300000

Version 1.7.2                                      April 2016                                            SCRM(1)

       scrm - An accurate coalescent simulator for genome-scale sequences

Recombination:-rRL Set recombination rate to R and locus length to L.

       -srpR
              Change the recombination rate R at sequence position p.

       -ll   Set the approximation window length to l.

   PopulationStructure:-Inpops1 ... sn [M]
              Use an island model with npop populations,

              where s1 to sn individuals are sampled each population.  Optionally assume a  symmetric  migration
              rate of M.

       -eIts1 ... sn [M]
              Sample s1 to sn indiviuals from their

              corresponding populations at time t.

       -MM   Assume a symmetric migration rate of M/(npop-1).

       -eMtM
              Change the symmetric migration rate to M/(npop-1) at time t.

       -mijM
              Set the migration rate from population j to population i to M

       -emtijM
              Set the migration rate from population j to

              population i to M at time t.

       -maM11M21 ...
              Sets the (backwards) migration matrix.

       -ematM11M21 ...
              Changes the migration matrix at time t

       -estip
              Population  admixture.  Replaces  a  fraction  of  1-p  of  population  i  with individuals a from
              population npop + 1 which is ignored afterwards (forward in time).

       -ejtij
              Speciation event at time t. Creates population j from individuals of population i.

   PopulationSizeChanges:-nin Set the present day size of population i to n*N0.

       -entin
              Change the size of population i to n*N0 at time t.

       -eNtn
              Set the present day size of all populations to n*N0.

       -gia Set the exponential growth rate of population i to a.

       -egtia
              Change the exponential growth rate of population i to a at time t.

       -Ga   Set the exponential growth rate of all populations to a.

       -eGta
              Change the exponential growth rate of all populations to a at time t.

   SummaryStatistics:-tTHETA
              Set the mutation rate to THETA = 4N_0u, where u is the neutral mutation rate per locus.

       -T     Print the local genealogies in newick format.

       -O     Print the local genealogies in the Oriented Forest format.

       -L     Print the TMRCA and the local tree length for each segment.

       -oSFS  Print the site frequency spectrum. Requires to set the mutation rate.

       -SC[ms|rel|abs]
              Scaling of sequence positions. Either relative to the locus length between 0 and 1 (rel), absolute
              in base pairs (abs) or ms-like (ms).

   Other:-seedSEED [SEED2SEED3]
              The random seed to use. Takes up three integer numbers.

       -v, --version
              Prints the version of scrm.

       -h, --help
              Prints this text.

       -pdigits
              Number of significant digits used in output.

scrmnsampnloci [-hvL] [-rrecL [-ll] [-srbrec]... ] [-Inpops1 ... sn [M] [-eIts1 ... sn [M]]...
       [-MM] [-eMtM]...  [-mijM] [-emtijM]...  [-maM11M21...Mnn] [-ematM11M21...Mnn]...  [-estip]...   [-ejtij]...]  [-nin] [-entin]...  [-eNtin]...  [-gia] [-egtia]...  [-Gta]
       [-eGta]...  [-ttheta [-oSFS] [-stbtheta]... ] [-seedseed [seed2seed3]] [-pdigits]