START_PARTITION_ALN
example.phy example.nex
d59_8.phy d59_8.nex
d69_31.phy d69_31.nex
END_PARTITION_ALN

START_SINGLE_ALN
d59_8.phy
d69_31.phy
example.phy
prot_M126_27_269.phy
END_SINGLE_ALN

START_PARTITION_OPTIONS
-sp
-spp
-spj
END_PARTITION_OPTIONS

START_GENERIC_OPTIONS
-m TEST
-m TESTNEW
-m TEST -bb 10000 -alrt 1000 -lbp 1000
-m TESTNEW -bb 10000 -alrt 1000 -lbp 1000
-m TEST -b 100
-m TESTNEW -b 100
END_GENERIC_OPTIONS
