msutils

This is an unofficial installer of the coalescent simulator ms. It builds ms with a decent random number generator, a variant of Mersenne Twister called dSFMT, instead of the original drand48() and rand().

Hudson, R. R. (2002) "Generating samples under a Wright-Fisher neutral model of genetic variation" Bioinformatics 18, 2

Usage

First, download ms.tar.gz manually from the official website. Then,

git clone https://github.com/heavywatal/msutils.git
cd msutils/
tar xzf ~/Downloads/ms.tar.gz
make
make install DESTDIR=${HOME}/local/bin

Test:

ms
ms 4 2 -t 5.0
ms 30 4 -t 3.0 | sample_stats

sample_stats++

sample_stats++ processes the output of ms and calculates some summary statistics as the original sample_stats does. But the output is simpler and can be saved as a pure TSV file.

ms 30 4 -t 3.0 | sample_stats++
# pi      S       D       tH
# 5.328736        16      1.084781        4.740230
# 2.471264        12      -0.600858       0.632184
# 11.857471       28      2.435626        10.901149
# 8.510345        22      1.873420        7.213793

If the samples are generated under a model with population structure, ms ... -I npop n1 n2 ..., summary statistics are calculated for each subpopulation.

ms 30 4 -t 3.0 -I 2 24 6 -ej 0.5 1 2 | sample_stats++
# pi_1    S_1     D_1     tH_1    pi_2    S_2     D_2     tH_2    Fst
# 3.858696        14      0.102469        4.228261        2.066667        5       -0.314657    0.733333        0.579264
# 6.173913        18      1.013146        5.304348        2.266667        4       1.593189     1.733333        0.276522
# 1.735507        10      -1.174108       1.307971        3.000000        9       -1.422837    5.400000        0.488053
# 5.438406        18      0.462681        6.996377        6.866667        14      0.736375     7.933333        0.047349

Use summstats if you want summary statistics of whole population:

ms 30 4 -t 3.0 -I 2 24 6 -ej 0.5 1 2 | summstats
# pi      S       D       tH
# 3.627586        20      -0.980626       1.475862
# 4.696552        16      0.553175        3.924138
# 3.321839        16      -0.602825       2.540230
# 7.873563        20      1.949895        7.367816

The program is written in C++ using molpopgen/libsequence.

brew install brewsci/bio/libsequence
make libseq
make install-libseq

You may need to modify LIBSEQUENCE variable if you installed libsequence manually without Homebrew, e.g.,

make LIBSEQUENCE=${HOME}/local libseq