# Ms-Teaching

### Category

Bioinformatics

### Program On

Teaching

### Version

20140304 (latest recorded change was made on Mar. 4, 2014.)

### Author / Distributor

Richard Hudson

### Description

Program to generates samples of gametes. For more information, please see https://uchicago.app.box.com/s/l3e5uf13tikfjm7e1il1eujitlsjdx13 (and the msdoc.pdf file there).

### Running Program

- Version 20140304 is installed at /usr/local/apps/gb/ms/20140304

To use this version, please load the module with

ml ms/20140304

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash

#SBATCH --job-name=__msjob__

#SBATCH --partition=batch

#SBATCH --mail-type=ALL

#SBATCH --mail-user=__username@uga.edu__

#SBATCH --ntasks=__1__

#SBATCH --mem=__2gb__

#SBATCH --time=__08:00:00__

#SBATCH --output=__ms__.%j.out

#SBATCH --error=__ms__.%j.err

cd $SLURM_SUBMIT_DIR

ml ms/20140304

ms __[options]__

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh

### Documentation

The manual msdoc.pdf is available in the directory /usr/local/apps/gb/ms/20140304/ms

ml ms/20140304 ms --help Too few command line arguments usage: ms nsam howmany Options: -t theta (this option and/or the next must be used. Theta = 4*N0*u ) -s segsites ( fixed number of segregating sites) -T (Output gene tree.) -F minfreq Output only sites with freq of minor allele >= minfreq. -r rho nsites (rho here is 4Nc) -c f track_len (f = ratio of conversion rate to rec rate. tracklen is mean length.) if rho = 0., f = 4*N0*g, with g the gene conversion rate. -G alpha ( N(t) = N0*exp(-alpha*t) . alpha = -log(Np/Nr)/t -I npop n1 n2 ... [mig_rate] (all elements of mig matrix set to mig_rate/(npop-1) -m i j m_ij (i,j-th element of mig matrix set to m_ij.) -ma m_11 m_12 m_13 m_21 m_22 m_23 ...(Assign values to elements of migration matrix.) -n i size_i (popi has size set to size_i*N0 -g i alpha_i (If used must appear after -M option.) The following options modify parameters at the time 't' specified as the first argument: -eG t alpha (Modify growth rate of all pop's.) -eg t i alpha_i (Modify growth rate of pop i.) -eM t mig_rate (Modify the mig matrix so all elements are mig_rate/(npop-1) -em t i j m_ij (i,j-th element of mig matrix set to m_ij at time t ) -ema t npop m_11 m_12 m_13 m_21 m_22 m_23 ...(Assign values to elements of migration matrix.) -eN t size (Modify pop sizes. New sizes = size*N0 ) -en t i size_i (Modify pop size of pop i. New size of popi = size_i*N0 .) -es t i proportion (Split: pop i -> pop-i + pop-npop, npop increases by 1. proportion is probability that each lineage stays in pop-i. (p, 1-p are admixt. proport. Size of pop npop is set to N0 and alpha = 0.0 , size and alpha of pop i are unchanged. -ej t i j ( Join lineages in pop i and pop j into pop j size, alpha and M are unchanged. -eA t popi num ( num Ancient samples from popi at time t -f filename ( Read command line arguments from file filename.) -p n ( Specifies the precision of the position output. n is the number of digits after the decimal.) -a (Print out allele ages.) See msdoc.pdf for explanation of these parameters.

### Installation

Source code is obtained from https://uchicago.app.box.com/s/l3e5uf13tikfjm7e1il1eujitlsjdx13 and compiled using rand1.c

### System

64-bit Linux