-
Notifications
You must be signed in to change notification settings - Fork 0
/
sample.stree6
221 lines (208 loc) · 7.8 KB
/
sample.stree6
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
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
#nexus [SplitsTree6]
BEGIN SPLITSTREE6;
DIMENSIONS nDataNodes=7 nAlgorithms=4;
PROGRAM version='SplitsTree CE (version 6.2.1-beta, built 16 Nov 2023)';
WORKFLOW creationDate='1709469336516'; [Sun Mar 03 20:35:36 CST 2024]
END; [SPLITSTREE6]
[
Methods:
Analysis was performed using SplitsTree CE 6.0.0_alpha (Huson and Bryant 2006).
The original input consisted of 12 taxa and a 12 x 12 distance matrix.
The Neighbor Net method (Bryant & Moulton 2004, Bryant & Huson 2023) was used (default options) so as to obtain 32 splits, cyclic.
The Show Splits method was used (default options) so as to obtain a Splits Network visualization.
References:
Bryant & Huson 2023: D. Bryant and D.H. Huson, NeighborNet- improved algorithms and implementation. Front. Bioinform. 3, 2023
Bryant & Moulton 2004: D. Bryant and V. Moulton. Neighbor-net: An agglomerative method for the construction of phylogenetic networks. Molecular Biology and Evolution, 21(2):255– 265, 2004.
Huson and Bryant 2006: D.H. Huson and D. Bryant. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution, 23:254–267, 2006.
]
BEGIN TAXA;
TITLE 'Input Taxa';
DIMENSIONS ntax=12;
TAXLABELS
[1] 'UIGHUR_XINJIANG_YILI_YINING'
[2] 'KAZAKH_XINJIANG_HABAHE'
[3] 'KAZAKH_XINJIANG_CHABUCHAER'
[4] 'KIRGHIZ_XINJIANG_KEZILESU'
[5] 'UZBEK_XINJIANG_ULUMUQI'
[6] 'TATAR_XINJIANG_ULUMUQI'
[7] 'TUVA_XINJIANG_ALETAI_BUERJIN'
[8] 'SALAER_QINGHAI_HAIDONG_XUNHUA'
[9] 'YUGU_GANSU_SUNAN_LIANHUA'
[10] 'AYNU'
[11] 'UYGHUR'
[12] 'WEST_YUGUR'
;
DISPLAYLABELS
[1] '<c 0x00ffffff><bg 0x00000000>UIGHUR_XINJIANG_YILI_YINING'
[2] '<c 0x00ffffff><bg 0x00000000>KAZAKH_XINJIANG_HABAHE'
[3] '<c 0x00ffffff><bg 0x00000000>KAZAKH_XINJIANG_CHABUCHAER'
[4] '<c 0x0000ffff><bg 0x00000000>KIRGHIZ_XINJIANG_KEZILESU'
[5] '<c 0x0000ffff><bg 0x00000000>UZBEK_XINJIANG_ULUMUQI'
[6] '<c 0x0000ffff><bg 0x00000000>TATAR_XINJIANG_ULUMUQI'
[7] '<c 0x0000ffff><bg 0x00000000>TUVA_XINJIANG_ALETAI_BUERJIN'
[8] '<c 0xff0000ff><bg 0x00000000>SALAER_QINGHAI_HAIDONG_XUNHUA'
[9] '<c 0xff0000ff><bg 0x00000000>YUGU_GANSU_SUNAN_LIANHUA'
[10] '<c 0xff0000ff><bg 0x00000000>AYNU'
[11] '<c 0x00ff00ff><bg 0x00000000>UYGHUR'
[12] '<c 0x00ff00ff><bg 0x00000000>WEST_YUGUR'
;
[TAXINFO;]
END; [TAXA]
BEGIN ALGORITHM;
TITLE 'Taxa Filter';
NAME 'Taxa Filter';
OPTIONS
;
END; [ALGORITHM]
BEGIN TAXA;
TITLE 'Working Taxa';
LINK ALGORITHM = 'Taxa Filter';
DIMENSIONS ntax=12;
TAXLABELS
[1] 'UIGHUR_XINJIANG_YILI_YINING'
[2] 'KAZAKH_XINJIANG_HABAHE'
[3] 'KAZAKH_XINJIANG_CHABUCHAER'
[4] 'KIRGHIZ_XINJIANG_KEZILESU'
[5] 'UZBEK_XINJIANG_ULUMUQI'
[6] 'TATAR_XINJIANG_ULUMUQI'
[7] 'TUVA_XINJIANG_ALETAI_BUERJIN'
[8] 'SALAER_QINGHAI_HAIDONG_XUNHUA'
[9] 'YUGU_GANSU_SUNAN_LIANHUA'
[10] 'AYNU'
[11] 'UYGHUR'
[12] 'WEST_YUGUR'
;
DISPLAYLABELS
[1] 'UIGHUR_XINJIANG_YILI_YINING'
[2] 'KAZAKH_XINJIANG_HABAHE'
[3] 'KAZAKH_XINJIANG_CHABUCHAER'
[4] 'KIRGHIZ_XINJIANG_KEZILESU'
[5] 'UZBEK_XINJIANG_ULUMUQI'
[6] 'TATAR_XINJIANG_ULUMUQI'
[7] 'TUVA_XINJIANG_ALETAI_BUERJIN'
[8] 'SALAER_QINGHAI_HAIDONG_XUNHUA'
[9] 'YUGU_GANSU_SUNAN_LIANHUA'
[10] 'AYNU'
[11] 'UYGHUR'
[12] 'WEST_YUGUR'
;
[TAXINFO;]
END; [TAXA]
BEGIN DISTANCES;
TITLE 'Input Distances';
LINK ALGORITHM = 'Taxa Filter';
DIMENSIONS ntax=12;
FORMAT labels=left diagonal triangle=Lower;
MATRIX
[1] 'UIGHUR_XINJIANG_YILI_YINING' 0
[2] 'KAZAKH_XINJIANG_HABAHE' 6.164 0
[3] 'KAZAKH_XINJIANG_CHABUCHAER' 4.917 3.786 0
[4] 'KIRGHIZ_XINJIANG_KEZILESU' 4.183 4.524 2.333 0
[5] 'UZBEK_XINJIANG_ULUMUQI' 3.634 5.503 3.674 3.406 0
[6] 'TATAR_XINJIANG_ULUMUQI' 4.263 5.116 3.242 3.281 3.502 0
[7] 'TUVA_XINJIANG_ALETAI_BUERJIN' 6.86 6.737 5.435 5.438 5.978 6.491 0
[8] 'SALAER_QINGHAI_HAIDONG_XUNHUA' 5.671 6.996 5.717 5.613 5.683 5.627 6.226 0
[9] 'YUGU_GANSU_SUNAN_LIANHUA' 6.684 6.253 5.878 6.072 6.085 6.168 6.536 5.326 0
[10] 'AYNU' 8.898 9.438 9.165 9.309 9.33 9.179 9.276 9.497 9.567 0
[11] 'UYGHUR' 3.837 6.537 5.977 5.353 5.519 5.672 7.545 6.552 6.915 9.58 0
[12] 'WEST_YUGUR' 6.532 7.406 6.711 6.78 6.715 6.909 7.993 7.453 5.677 9.566 7.27 0
;
END; [DISTANCES]
BEGIN ALGORITHM;
TITLE 'Input Data Filter';
LINK DISTANCES = 'Input Distances';
NAME 'Distances Taxa Filter';
END; [ALGORITHM]
BEGIN DISTANCES;
TITLE 'Working Distances';
LINK ALGORITHM = 'Input Data Filter';
DIMENSIONS ntax=12;
FORMAT labels=left diagonal triangle=Lower;
MATRIX
[1] 'UIGHUR_XINJIANG_YILI_YINING' 0
[2] 'KAZAKH_XINJIANG_HABAHE' 6.164 0
[3] 'KAZAKH_XINJIANG_CHABUCHAER' 4.917 3.786 0
[4] 'KIRGHIZ_XINJIANG_KEZILESU' 4.183 4.524 2.333 0
[5] 'UZBEK_XINJIANG_ULUMUQI' 3.634 5.503 3.674 3.406 0
[6] 'TATAR_XINJIANG_ULUMUQI' 4.263 5.116 3.242 3.281 3.502 0
[7] 'TUVA_XINJIANG_ALETAI_BUERJIN' 6.86 6.737 5.435 5.438 5.978 6.491 0
[8] 'SALAER_QINGHAI_HAIDONG_XUNHUA' 5.671 6.996 5.717 5.613 5.683 5.627 6.226 0
[9] 'YUGU_GANSU_SUNAN_LIANHUA' 6.684 6.253 5.878 6.072 6.085 6.168 6.536 5.326 0
[10] 'AYNU' 8.898 9.438 9.165 9.309 9.33 9.179 9.276 9.497 9.567 0
[11] 'UYGHUR' 3.837 6.537 5.977 5.353 5.519 5.672 7.545 6.552 6.915 9.58 0
[12] 'WEST_YUGUR' 6.532 7.406 6.711 6.78 6.715 6.909 7.993 7.453 5.677 9.566 7.27 0
;
END; [DISTANCES]
BEGIN ALGORITHM;
TITLE 'Neighbor Net';
LINK DISTANCES = 'Working Distances';
NAME 'Neighbor Net';
OPTIONS
InferenceAlgorithm = 'ActiveSet';
END; [ALGORITHM]
BEGIN SPLITS;
TITLE 'Splits';
LINK ALGORITHM = 'Neighbor Net';
DIMENSIONS ntax=12 nsplits=32;
FORMAT labels=no weights=yes confidences=no;
PROPERTIES fit=99.9 cyclic;
CYCLE 1 5 6 4 3 2 12 9 8 7 10 11;
MATRIX
[1, size=1] 1.01405344 1,
[2, size=2] 0.76986088 1 11,
[3, size=3] 0.16998447 1 10 11,
[4, size=5] 0.16988877 1 7 8 9 10 11 12,
[5, size=4] 0.1643407 1 2 7 8 9 10 11 12,
[6, size=1] 1.37015191 1 2 3 4 6 7 8 9 10 11 12,
[7, size=1] 2.23683057 1 2 3 4 5 6 7 8 9 10 12,
[8, size=5] 0.25397301 1 3 4 5 6,
[9, size=3] 0.10568184 1 5 6,
[10, size=2] 0.25042598 1 5,
[11, size=1] 5.87411191 1 2 3 4 5 6 7 8 9 11 12,
[12, size=2] 0.27483692 1 2 3 4 5 6 8 9 11 12,
[13, size=5] 0.1345841 1 2 3 4 5 6 11,
[14, size=5] 0.21406404 1 4 5 6 11,
[15, size=3] 0.03583032 1 5 11,
[16, size=1] 3.02197665 1 2 3 4 5 6 8 9 10 11 12,
[17, size=2] 0.02813038 1 2 3 4 5 6 9 10 11 12,
[18, size=3] 0.16969986 1 2 3 4 5 6 10 11 12,
[19, size=1] 2.50250332 1 2 3 4 5 6 7 9 10 11 12,
[20, size=2] 0.40667705 1 2 3 4 5 6 7 10 11 12,
[21, size=1] 1.94496825 1 2 3 4 5 6 7 8 10 11 12,
[22, size=2] 0.73234611 1 2 3 4 5 6 7 8 10 11,
[23, size=3] 0.12562682 1 3 4 5 6 7 8 10 11,
[24, size=1] 3.15754692 1 2 3 4 5 6 7 8 9 10 11,
[25, size=1] 2.19893964 1 3 4 5 6 7 8 9 10 11 12,
[26, size=2] 0.34752397 1 4 5 6 7 8 9 10 11 12,
[27, size=3] 0.19409975 1 5 6 7 8 9 10 11 12,
[28, size=4] 0.22481508 1 5 7 8 9 10 11 12,
[29, size=1] 0.80291046 1 2 4 5 6 7 8 9 10 11 12,
[30, size=2] 0.23789141 1 2 5 6 7 8 9 10 11 12,
[31, size=1] 0.98172901 1 2 3 5 6 7 8 9 10 11 12,
[32, size=1] 1.54206049 1 2 3 4 5 7 8 9 10 11 12,
;
END; [SPLITS]
BEGIN ALGORITHM;
TITLE 'Show Splits';
LINK SPLITS = 'Splits';
NAME 'Show Splits';
OPTIONS
View = 'SplitsNetwork';
END; [ALGORITHM]
BEGIN VIEW;
TITLE 'SplitsNetwork';
LINK ALGORITHM = 'Show Splits';
NAME 'SplitsNetwork';
INPUT 'SPLITS';
OPTIONS
Diagram = 'Splits',
Orientation = 'Rotate0Deg',
Rooting = 'None',
ZoomFactor = 12.55283196,
FontScaleFactor = 1,
RootAngle = 160,
OutlineFill = 0xc0c0c0ff,
Edits = 'c:1:0x00ffffff' 'c:25:0x00ffffff' 'c:29:0x00ffffff' 'c:31:0x0000ffff' 'c:6:0x0000ffff' 'c:32:0x0000ffff' 'c:16:0x0000ffff' 'c:19:0xff0000ff' 'c:21:0xff0000ff' 'c:11:0xff0000ff' 'c:7:0x00ff00ff' 'c:24:0x00ff00ff',
ShowConfidence = 'false',
ActiveTraits = '*All*';
END; [VIEW]