Hi Hirra,
The assignment is not random, it follows the order of the sequences in the data:
- Seqs. A and B are compared and found to be identical so they are both
assigned to haplotype I.
- Seq. C is compared to haplotype I (effectively seq. A) and found to be
different so it is assigned to
Dear Carolina.
After running make.simmap with nsim=100 or more, just run summary( ) on
your "multiSimmap" object and then plot the result. For instance:
map.trees<-make.simmap(tree,x,model="SYM",nsim=200)
map.summary<-summary(map.trees)
print(map.summary)
