SYNOPSIS

scrm nsamp nloci [-hvL] [-r rec L [-l l] [-sr b rec]... ] [-I npop s1 ... sn [M] [-eI t s1 ... sn [M]]... [-M M] [-eM t M]... [-m i j M] [-em t i j M]... [-ma M11 M21 ... Mnn] [-ema t M11 M21 ... Mnn]... [-es t i p]... [-ej t i j]...] [-n i n] [-en t i n]... [-eN t i n]... [-g i a] [-eg t i a]... [-G t a] [-eG t a]... [-t theta [-oSFS] [-st b theta]... ] [-seed seed [seed2 seed3]] [-p digits]

DESCRIPTION

scrm is a coalescent simulator for biological sequences. Different to similar 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.

OPTIONS

Recombination:

-r R L

Set recombination rate to R and locus length to L.

-sr p R

Change the recombination rate R at sequence position p.

-l l

Set the approximation window length to l.

Population Structure:

-I npop s1 ... 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.

-eI t s1 ... sn [M]

Sample s1 to sn indiviuals from their

corresponding populations at time t.

-M M

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

-eM t M

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

-m i j M

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

-em t i j M

Set the migration rate from population j to

population i to M at time t.

-ma M11 M21 ...

Sets the (backwards) migration matrix.

-ema t M11 M21 ...

Changes the migration matrix at time t

-es t i p

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).

-ej t i j

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

Population Size Changes:

-n i n

Set the present day size of population i to n*N0.

-en t i n

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

-eN t n

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

-g i a

Set the exponential growth rate of population i to a.

-eg t i a

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

-G a

Set the exponential growth rate of all populations to a.

-eG t a

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

Summary Statistics:

-t THETA

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:

-seed SEED [SEED2 SEED3]

The random seed to use. Takes up three integer numbers.

-v, --version

Prints the version of scrm.

-h, --help

Prints this text.

-p digits

Number of significant digits used in output.

Examples

Five independent sites for 10 individuals using Kingman's Coalescent:

scrm 10 5 -t 10

A sequence of 10kb from 4 individuals under the exact ARG:

scrm 4 1 -t 10 -r 4 10000

A sequence of 100Mb using the SMC' approximation:

scrm 4 1 -t 10 -r 4000 100000000 -l 0

Same as above, but with essentially correct linkage:

scrm 4 1 -t 10 -r 4000 100000000 -l 300000