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
So, block M
contains several strings that belongs to one category, where strings in block M1
are ATCG
and TCAA
, M2 has strings TCAA
and GAGT
. Similarly, block S
also has 4 total strings.
Hybrid blocks
have two strings (ATCG
and CAGT
) where one of the strings is from block M
and another strings is from block S
.
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 block S
.
Thanks,