**************************************** Welcome to the Morphy Test Interface **************************************** Missing data includes lowest order bit (1...1111). argv[0] == /Users/TGuillerme/Xcode/Morphy-dhtyrombwhsciqcfglwxmrvwnmbc/Build/Products/Debug/Morphy... Testing matrices: No symbols list supplied. Attempting to estimate state number from input matrix. Using the joint ctypes: 1 The newick string processed: UNTITLED = [&R] ((((((1,2),3),4),5),6),(7,(8,(9,(10,(11,12)))))); Newick string is rooted ====== Enter the optimisation ===== Node: 18 1st Down: left = c(1) 1st Down: right = c(-) 1st Down: node = c(-,1) Node: 17 1st Down: left = c(-,1) 1st Down: right = c(-) 1st Down: node = c(-) Node: 16 1st Down: left = c(-) 1st Down: right = c(-) 1st Down: node = c(-) Node: 15 1st Down: left = c(-) 1st Down: right = c(1) 1st Down: node = c(-,1) Node: 14 1st Down: left = c(-,1) 1st Down: right = c(1) 1st Down: node = c(1) Node: 23 1st Down: left = c(-) 1st Down: right = c(1) 1st Down: node = c(-,1) Node: 22 1st Down: left = c(-) 1st Down: right = c(-,1) 1st Down: node = c(-) Node: 21 1st Down: left = c(-) 1st Down: right = c(-) 1st Down: node = c(-) Node: 20 1st Down: left = c(1) 1st Down: right = c(-) 1st Down: node = c(-,1) Node: 19 1st Down: left = c(1) 1st Down: right = c(-,1) 1st Down: node = c(1) Node: 13 1st Down: left = c(1) 1st Down: right = c(1) 1st Down: node = c(1) Here's the length after the downpass: 0 BEGIN TEST tui_check_broken_tree() == PASS == tui_check_broken_tree(): input tree connections verified OK END broken tree test Node: 13 1st Up: ancestor = c(1) 1st Up: left = c(1) 1st Up: right = c(1) 1st Up: node = c(1) Node: 14 1st Up: ancestor = c(1) 1st Up: left = c(-,1) 1st Up: right = c(1) 1st Up: node = c(1) Node: 15 1st Up: ancestor = c(1) 1st Up: left = c(-) 1st Up: right = c(1) 1st Up: node = c(1) Node: 16 1st Up: ancestor = c(1) 1st Up: left = c(-) 1st Up: right = c(-) 1st Up: node = c(-) Node: 17 1st Up: ancestor = c(-) 1st Up: left = c(-,1) 1st Up: right = c(-) 1st Up: node = c(-) Node: 18 1st Up: ancestor = c(-) 1st Up: left = c(1) 1st Up: right = c(-) 1st Up: node = c(-) Node: 18 2nd Down: left = c(1) 2nd Down: right = c(-) 2nd Down: node = c(-) Node: 17 2nd Down: left = c(-) 2nd Down: right = c(-) 2nd Down: node = c(-) Node: 16 2nd Down: left = c(-) 2nd Down: right = c(-) 2nd Down: node = c(-) Node: 15 2nd Down: left = c(-) 2nd Down: right = c(1) 2nd Down: node = c(1) Node: 14 2nd Down: left = c(1) 2nd Down: right = c(1) 2nd Down: node = c(1) Node: 19 1st Up: ancestor = c(1) 1st Up: left = c(1) 1st Up: right = c(-,1) 1st Up: node = c(1) Node: 20 1st Up: ancestor = c(1) 1st Up: left = c(1) 1st Up: right = c(-) 1st Up: node = c(1) Node: 21 1st Up: ancestor = c(1) 1st Up: left = c(-) 1st Up: right = c(-) 1st Up: node = c(-) Node: 22 1st Up: ancestor = c(-) 1st Up: left = c(-) 1st Up: right = c(-,1) 1st Up: node = c(-) Node: 23 1st Up: ancestor = c(-) 1st Up: left = c(-) 1st Up: right = c(1) 1st Up: node = c(-) Node: 23 2nd Down: left = c(-) 2nd Down: right = c(1) 2nd Down: node = c(-) Node: 22 2nd Down: left = c(-) 2nd Down: right = c(-) 2nd Down: node = c(-) Node: 21 2nd Down: left = c(-) 2nd Down: right = c(-) 2nd Down: node = c(-) Node: 20 2nd Down: left = c(1) 2nd Down: right = c(-) 2nd Down: node = c(1) Node: 19 2nd Down: left = c(1) 2nd Down: right = c(1) 2nd Down: node = c(1) Node: 13 2nd Down: left = c(1) 2nd Down: right = c(1) 2nd Down: node = c(1) Node: 13 2nd Up: ancestor = c(1) 2nd Up: left = c(1) 2nd Up: right = c(1) 2nd Up: node = c(1) Node: 14 2nd Up: ancestor = c(1) 2nd Up: left = c(1) 2nd Up: right = c(1) 2nd Up: node = c(1) Node: 15 2nd Up: ancestor = c(1) 2nd Up: left = c(-) 2nd Up: right = c(1) 2nd Up: node = c(1) Node: 16 2nd Up: ancestor = c(1) 2nd Up: left = c(-) 2nd Up: right = c(-) 2nd Up: node = c(-) Node: 17 2nd Up: ancestor = c(-) 2nd Up: left = c(-) 2nd Up: right = c(-) 2nd Up: node = c(-) Node: 18 2nd Up: ancestor = c(-) 2nd Up: left = c(1) 2nd Up: right = c(-) 2nd Up: node = c(-) Node: 19 2nd Up: ancestor = c(1) 2nd Up: left = c(1) 2nd Up: right = c(1) 2nd Up: node = c(1) Node: 20 2nd Up: ancestor = c(1) 2nd Up: left = c(1) 2nd Up: right = c(-) 2nd Up: node = c(1) Node: 21 2nd Up: ancestor = c(1) 2nd Up: left = c(-) 2nd Up: right = c(-) 2nd Up: node = c(-) Node: 22 2nd Up: ancestor = c(-) 2nd Up: left = c(-) 2nd Up: right = c(-) 2nd Up: node = c(-) Node: 23 2nd Up: ancestor = c(-) 2nd Up: left = c(-) 2nd Up: right = c(1) 2nd Up: node = c(-) Node: 1st Down: left = c(1) 1st Down: right = c(1) 1st Down: node = c(1) Node: 1st Down: left = c(1) 1st Down: right = c(1) 1st Down: node = c(1) Node: 1st Down: left = c(-) 1st Down: right = c(1) 1st Down: node = c(-,1) Node: 1st Down: left = c(-) 1st Down: right = c(-,1) 1st Down: node = c(-) Node: 1st Down: left = c(-) 1st Down: right = c(-) 1st Down: node = c(-) Node: 1st Down: left = c(-) 1st Down: right = c(1) 1st Down: node = c(-,1) Node: 1st Down: left = c(-,1) 1st Down: right = c(-,1) 1st Down: node = c(-,1) Node: 1st Down: left = c(1) 1st Down: right = c(-) 1st Down: node = c(-,1) Node: 1st Down: left = c(1) 1st Down: right = c(-) 1st Down: node = c(-,1) Node: 1st Down: left = c(1) 1st Down: right = c(-,1) 1st Down: node = c(1) Node: 1st Down: left = c(-,1) 1st Down: right = c(1) 1st Down: node = c(1) Node: 1st Down: left = c(1) 1st Down: right = c(1) 1st Down: node = c(1) Node: 1st Down: left = c(-) 1st Down: right = c(1) 1st Down: node = c(-,1) Node: 1st Down: left = c(1) 1st Down: right = c(1) 1st Down: node = c(1) Node: 1st Down: left = c(-) 1st Down: right = c(1) 1st Down: node = c(-,1) Node: 1st Down: left = c(1) 1st Down: right = c(-) 1st Down: node = c(-,1) Node: 1st Down: left = c(-,1) 1st Down: right = c(-,1) 1st Down: node = c(-,1) Node: 1st Down: left = c(-,1) 1st Down: right = c(-) 1st Down: node = c(-) Node: 1st Down: left = c(1) 1st Down: right = c(-) 1st Down: node = c(-,1) Node: 1st Down: left = c(-) 1st Down: right = c(-) 1st Down: node = c(-) Here's the length after the uppass: 2 ====== Exit the optimisation ===== =================== Expected: 2 Calculated: 2 =================== SUMMARY: Test of all topologies for matrix 1---1111---1; concluded All tests PASSED (lldb)