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 = ((t5,t1),(t7,(t6,(t8,t9,('t2 the name',('one should be punished, for (that)!','isn''that [a] strange name?'))))));
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              []      0.0     106.84        -
  2          -               4          [3, 1]    100.0     106.84     10.0
  3 'one should be punished, for (that)!'               2              []      0.5     107.34        -
  4          -               6          [5, 2]      0.4       6.84      0.3
  5 't2 the name'               4              []      0.3       7.14        -
  6          -               9       [7, 8, 4]      4.0       6.44      3.0
  7         t8               6              []      1.2       7.64        -
  8         t9               6        [17, 18]      3.4       9.84        -
  9          -              11         [10, 6]      2.0       2.44      1.0
 10         t6               9              []      1.0       3.44        -
 11          -              16         [12, 9]     0.44       0.44     33.0
 12         t7              11              []     99.9     100.34        -
 13          -              16        [14, 15]     13.0       13.0     12.0
 14         t5              13              []     99.0      112.0        -
 15         t1              13              []     0.98      13.98        -
 16          -            None        [13, 11]        -          -        -
 17        t90               8              []      1.0      10.84        -
 18        t91               8              []      1.0      10.84        -

Root:  16
self incompatibility...: []
ok

----------------------------------------------------------------------
Ran 2 tests in 0.158s

OK
