(*Custom Alphabet Character Analysis*)

read(custom_alphabet:("ca1.fas",tcm:("m1.mat")))
transform(level:3)
build(all,10)
swap()
fuse(iterations:5,replace:best,keep:5,swap())
select()
set(root:"One")
report("CA1_trees.tre",trees:(total),"CA1_cs.pdf",graphconsensus)
quit()