Please compile the msmfs according to the documentation of ms (The most convenient way is typing ./clms).
Please ignore the warning messages during installation. 

The usage of msmfs is the same as ms, except the following added options:

[1] -Y singleton doubleton tripleton  (fixed number of MFS)
[2] -U 1/0 (1 represents unfolded MFS; 0 represents folded MFS. Default is 1.)
[3] -H 0/1 mhlength (0 represents no multiple hits; 1 represents multiple hits. Default is 0. If you specify 1, you must specify 'mhlength'.)
[4] -X quesMarkNum qmOnepos qmTwopos qmThreepos ...These positions are column-based. The number of first column is 1,2,3...nsam. The number of second column is nsam+1, nsam+2, 2*nsam. We recommend to use the which function in R to obtain question marks index (i.e., which(yourData == '?'))