Hi.. i have data for two groups.. one group has 10 diffent strains and other group has 5 different strains. 40 genes are selected and primers are designed for these genes. Sequencing is performed on these amplicons which has length of around 300bp. Now i need to identify haplotypes by mapping them to the reference genes. I have to identify haplotypes for each strain as well across the strains. The data i have is reference genes and 454 reads. How to proceed please suggest me.
Tried to use some softwares like Haploview, hapcut, etc..