I've made a question about supertrees.
My goal is to integrate data from SNPs (DNA), MIRUs (multi -range around 1 to 25) and Spoligotype (binary) and eventually RFLPs, into a single tree.
@Dan Gaston suggested to use RAxML to obtain the same output.
I've been reading and for I what I understood I need the give a file with all the data (example file that I've created to test) and a partition file.
(I'm testing only with binary and dna data, for now)
In the command line:
./raxmlHPC-PTHREADS-SSE3 -m BINGAMMA -q partition_file.txt -s phylip_file.phy -n Test -T 2
but it gives me a error:
ERROR: Bad base (2) at site 47 of sequence 1 Problem reading alignment file
command line and error:
./raxmlHPC-PTHREADS-SSE3 -m MULTIGAMMA -q test_part_all.txt -s test_all_types.phy -K ORDERED -n Multi -T 2 Multi State Error, characters must be used in the order they are available, i.e. 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V You are using the following caharcters: 0 1 2 3 4 A C G T
This is probably something easy that I'm not seeing.
Thank you guys!