I finally built a PHASE input file (.inp) and my analysis was executed successfully.
Now I have phased output which consists of several files:
- test4.out_freqs : haplotype frequency estimates
- test4.out_pairs : most likely haplotype pairs for each individual
- test4.out_recom : estimates of recombination parameters
- test4.out_monitor : file for monitoring convergence
I would like to visualize the haplotypes with HaploView.
Is there any tool or script which converts the output from PHASE to any HaploView format?