run_hyde.py -i data.txt -m map.txt -o out -n 16 -t 4 -s 50000

[yuanjigui]

what the -t 4 mean? does it includes outgroup ? I have sp1, sp2, sp3, sp4, and out 5 groups. what -t should be?

[pblischak]

The -t option is to specify the number of taxa, including the outgroup, so in your case it should be 5