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
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=${HOME}/local/binTest:
ms
ms 4 2 -t 5.0
ms 30 4 -t 3.0 | sample_statssample_stats++ processes the output of ms and calculates some summary statistics as the original sample_stats does. But the output is simpler and can be saved as a pure TSV file.
ms 30 4 -t 3.0 | sample_stats++
# pi S D tH
# 5.328736 16 1.084781 4.740230
# 2.471264 12 -0.600858 0.632184
# 11.857471 28 2.435626 10.901149
# 8.510345 22 1.873420 7.213793If the samples are generated under a model with population structure, ms ... -I npop n1 n2 ..., summary statistics are calculated for each subpopulation.
ms 30 4 -t 3.0 -I 2 24 6 -ej 0.5 1 2 | sample_stats++
# pi_1 S_1 D_1 tH_1 pi_2 S_2 D_2 tH_2 Fst
# 3.858696 14 0.102469 4.228261 2.066667 5 -0.314657 0.733333 0.579264
# 6.173913 18 1.013146 5.304348 2.266667 4 1.593189 1.733333 0.276522
# 1.735507 10 -1.174108 1.307971 3.000000 9 -1.422837 5.400000 0.488053
# 5.438406 18 0.462681 6.996377 6.866667 14 0.736375 7.933333 0.047349Use summstats if you want summary statistics of whole population:
ms 30 4 -t 3.0 -I 2 24 6 -ej 0.5 1 2 | summstats
# pi S D tH
# 3.627586 20 -0.980626 1.475862
# 4.696552 16 0.553175 3.924138
# 3.321839 16 -0.602825 2.540230
# 7.873563 20 1.949895 7.367816The program is written in C++ using molpopgen/libsequence.
brew install brewsci/bio/libsequence
make libseq
make install-libseqYou may need to modify LIBSEQUENCE variable if you installed libsequence manually without Homebrew, e.g.,
make LIBSEQUENCE=${HOME}/local libseq