In the following data, I am trying to run a simple markov model to find which haplotype came from which block.
block_M1 block_M2 hybrid_block block_S1 block_S2 A|T T|A A|C C|G T|A T|G C|T T|A A|T C|A C|A A|G C|G G|A C|G G|T A|T G|T C|T A|T
block M contains several strings that belongs to one category, where strings in
block M1 are
TCAA, M2 has strings
block S also has 4 total strings.
Hybrid blocks have two strings (
CAGT) where one of the strings is from
block M and another strings is from
I am trying to find a software which can take help with discriminating which string in the hybrid block came from block M vs. S. If not I want to build a markov model in python do so. Any suggestions? In this example I can tell that in hybrid block
ATCG came from
block M and
CAGT came from