test_Nexus Test Nexus module ... Name: Nexus/test_Nexus_input.nex 9 48 dna True ? - Taxa: t1 t2 the name isn'that [a] strange name? one should be punished, for (that)! t5 t6 t7 t8 t9 Charlabels: 0 a 1 b 2 c 4 f 9 A 10 B 22 x 23 y 29 1,2,3 can't decide for a name?! 47 final Charsets: big [0, 2, 4, 6] bigchunk [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46] byname [0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29] c1 [0, 1, 2, 3, 4, 5, 6, 7] c2 [8, 9, 10, 11, 12, 13, 14, 15] c3 [16, 17, 18, 19, 20, 21, 22, 23] firsthalf [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] mix [0, 1, 4, 7, 10, 13, 16, 19, 22, 25, 28, 31, 34, 37, 40, 43, 46] mux [0, 1, 4, 7, 8, 10, 13, 16, 17, 18, 19, 20, 21, 22, 23, 25, 28, 31, 34, 37, 40, 43, 46] pos1 [0, 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45] pos2 [1, 4, 7, 10, 13, 16, 19, 22, 25, 28, 31, 34, 37, 40, 43, 46] pos3 [2, 5, 8, 11, 14, 17, 20, 23, 26, 29, 32, 35, 38, 41, 44, 47] secondhalf [24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47] Taxsets: normal ["isn'that [a] strange name?", 'one should be punished, for (that)!', 't1', 't5', 't6', 't8'] reference ["isn'that [a] strange name?", 'one should be punished, for (that)!', 't1', 't2 the name', 't5', 't6'] tbyname1 ["isn'that [a] strange name?", 'one should be punished, for (that)!', 't1', 't2 the name', 't5', 't6'] tbyname2 ["isn'that [a] strange name?", 'one should be punished, for (that)!', 't2 the name', 't5', 't6', 't7'] tbyname3 ['t1', 't2 the name'] Charpartitions: codons: a [0, 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45] b [1, 4, 7, 10, 13, 16, 19, 22, 25, 28, 31, 34, 37, 40, 43, 46] c [2, 5, 8, 11, 14, 17, 20, 23, 26, 29, 32, 35, 38, 41, 44, 47] part: one [0, 1, 2, 3, 4, 5, 6, 7] three [16, 17, 18, 19, 20, 21, 22, 23] two [8, 9, 10, 11, 12, 13, 14, 15] Taxpartitions: taxpart: badnames ["isn'that [a] strange name?", 'one should be punished, for (that)!', 't2 the name'] goodnames ['t1', 't5', 't6', 't7', 't8', 't9'] Name: Nexus/f1.nex 7 4 dna False ? - Taxa: t2 the name isn'that [a] strange name? one should be punished, for (that)! t5 t6 t8 t9 Charlabels: 0 a 1 c 2 f Charsets: big [0, 1, 2, 3] bigchunk [1, 2, 3] byname [0, 2, 3] c1 [0, 1, 2, 3] firsthalf [0, 1, 2, 3] mix [0, 2] mux [0, 2] pos1 [0, 3] pos2 [2] pos3 [1] Taxsets: normal ["isn'that [a] strange name?", 'one should be punished, for (that)!', 't5', 't6', 't8'] reference ["isn'that [a] strange name?", 'one should be punished, for (that)!', 't2 the name', 't5', 't6'] tbyname1 ["isn'that [a] strange name?", 'one should be punished, for (that)!', 't2 the name', 't5', 't6'] tbyname2 ["isn'that [a] strange name?", 'one should be punished, for (that)!', 't2 the name', 't5', 't6'] tbyname3 ['t2 the name'] Charpartitions: codons: a [0, 3] b [2] c [1] part: one [0, 1, 2, 3] Taxpartitions: taxpart: badnames ["isn'that [a] strange name?", 'one should be punished, for (that)!', 't2 the name'] goodnames ['t5', 't6', 't8', 't9'] Name: Nexus/f2.nex 9 38 dna False ? - Taxa: t1 t2 the name isn'that [a] strange name? one should be punished, for (that)! t5 t6 t7 t8 t9 Charlabels: 0 a 1 b 2 c 3 f 7 A 8 B 17 x 22 1,2,3 can't decide for a name?! 37 final Charsets: big [0, 2, 3, 5] bigchunk [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36] byname [0, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] c1 [0, 1, 2, 3, 4, 5] c2 [6, 7, 8, 9, 10, 11] c3 [12, 13, 14, 15, 16, 17] firsthalf [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] mix [0, 1, 3, 8, 10, 12, 17, 19, 21, 26, 28, 30, 33, 36] mux [0, 1, 3, 6, 8, 10, 12, 13, 14, 15, 16, 17, 19, 21, 26, 28, 30, 33, 36] pos1 [0, 5, 7, 9, 14, 16, 18, 23, 25, 27, 32, 35] pos2 [1, 3, 8, 10, 12, 17, 19, 21, 26, 28, 30, 33, 36] pos3 [2, 4, 6, 11, 13, 15, 20, 22, 24, 29, 31, 34, 37] secondhalf [18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] Taxsets: normal ["isn'that [a] strange name?", 'one should be punished, for (that)!', 't1', 't5', 't6', 't8'] reference ["isn'that [a] strange name?", 'one should be punished, for (that)!', 't1', 't2 the name', 't5', 't6'] tbyname1 ["isn'that [a] strange name?", 'one should be punished, for (that)!', 't1', 't2 the name', 't5', 't6'] tbyname2 ["isn'that [a] strange name?", 'one should be punished, for (that)!', 't2 the name', 't5', 't6', 't7'] tbyname3 ['t1', 't2 the name'] Charpartitions: codons: a [0, 5, 7, 9, 14, 16, 18, 23, 25, 27, 32, 35] b [1, 3, 8, 10, 12, 17, 19, 21, 26, 28, 30, 33, 36] c [2, 4, 6, 11, 13, 15, 20, 22, 24, 29, 31, 34, 37] part: one [0, 1, 2, 3, 4, 5] three [12, 13, 14, 15, 16, 17] two [6, 7, 8, 9, 10, 11] Taxpartitions: taxpart: badnames ["isn'that [a] strange name?", 'one should be punished, for (that)!', 't2 the name'] goodnames ['t1', 't5', 't6', 't7', 't8', 't9'] usertype matrix_test stepmatrix=5 A C G T - [A] . 2.40 2.57 2.43 2.43 [C] 2.40 . 2.28 2.12 2.14 [G] 2.57 2.28 . 2.31 2.31 [T] 2.43 2.12 2.31 . 2.14 [-] 2.43 2.14 2.31 2.14 . ; ok Test Tree module. ... tree tree1 = (((((('one should be punished, for (that)!','isn''that [a] strange name?'),'t2 the name'),t8,t9),t6),t7),(t5,t1)); Monophyletic t6,t7,t8,t9: -1 Monophyletic t1,t5: 13 Subtree t1,t5: Set(['t5', 't1']) The tree looks as follows: # taxon prev succ brlen blen (sum) support 1 'isn''that [a] strange name?' 2 [] 100.0 119.84 10.0 2 - 4 [3, 1] 0.4 19.84 0.3 3 'one should be punished, for (that)!' 2 [] 0.5 20.34 - 4 - 6 [2, 5] 4.0 19.44 3.0 5 't2 the name' 4 [] 0.3 19.74 - 6 - 9 [4, 7, 8] 2.0 15.44 1.0 7 t8 6 [] 1.2 16.64 - 8 t9 6 [17, 18] 3.4 18.84 - 9 - 11 [6, 10] 0.44 13.44 33.0 10 t6 9 [] 1.0 14.44 - 11 - 16 [9, 12] 13.0 13.0 12.0 12 t7 11 [] 99.9 112.9 - 13 - 16 [14, 15] 0.0 0.0 0.0 14 t5 13 [] 99.0 99.0 - 15 t1 13 [] 0.98 0.98 - 16 - None [11, 13] 0.0 0.0 - 17 t90 8 [] 1.0 19.84 - 18 t91 8 [] 1.0 19.84 - Root: 16 self incompatibility...: [] ok ---------------------------------------------------------------------- Ran 2 tests in 0.163s OK