---
name: "scrm"
section: "1"
platform: "linux"
package: "scrm"
version: "1.7.4-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/scrm"
---

# scrm(1)

An accurate coalescent simulator for genome-scale sequences

## NAME

scrm - An accurate coalescent simulator for genome-scale sequences

## 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