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
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
|
# test datasets
nw_simple1 = '((A, (B,C)),D);'
nw_simple2 = '((D, (B,C)),A);'
nw_simple3 = '((B, (A,C)),D);'
nw_simple4 = '((A, (B,C)),D);'
nw_simple5 = '(H,(A,(B,C,D)),D,T,S,(U,Y));'
nw_simple6 = '(H,(A,(B,(C),(T))),D);'
nw_full = '(Ddi0002240:1.457468,Dme0014628:1.235133,(Aga0007658:1.752559,(Cin0011239:0.728210,((Fru0004507:0.184484,((Dre0008391:0.000000,Dre0008390:0.000000)1.000000:0.002729,Dre0008392:0.010931)1.000000:0.122420)1.000000:0.142530,((Xtr0044988:0.422481,(Gga0000982:0.000000,Gga0000981:0.000000)1.000000:0.109228)1.000000:0.035488,(Mdo0014718:0.129337,((Mms0024821:0.027982,Rno0030248:0.029287)1.000000:0.074667,((Cfa0016700:0.031643,Bta0018700:0.047366)1.000000:0.007962,(Ptr0000001:0.005433,((Hsa0010730:0.018311[&&NHX:flag=Red:mood=bad],Hsa0000001:0.003656)1.000000:0.007173,Hsa0010711:0.002730)1.000000:0.014995)1.000000:0.052577)1.000000:0.010070)1.000000:0.035671)1.000000:0.074417)1.000000:0.034385)1.000000:0.184380[&&NHX:flag=Black])1.000000:0.219467)1.000000:0.317782[&&NHX:flag=White]);'
nw_dflt = '(Ddi0002240:1.457468,Dme0014628:1.235133,(Aga0007658:1.752559,(Cin0011239:0.728210,((Fru0004507:0.184484,((Dre0008391:0.000000,Dre0008390:0.000000)1.000000:0.002729,Dre0008392:0.010931)1.000000:0.122420)1.000000:0.142530,((Xtr0044988:0.422481,(Gga0000982:0.000000,Gga0000981:0.000000)1.000000:0.109228)1.000000:0.035488,(Mdo0014718:0.129337,((Mms0024821:0.027982,Rno0030248:0.029287)1.000000:0.074667,((Cfa0016700:0.031643,Bta0018700:0.047366)1.000000:0.007962,(Ptr0000001:0.005433,((Hsa0010730:0.018311,Hsa0000001:0.003656)1.000000:0.007173,Hsa0010711:0.002730)1.000000:0.014995)1.000000:0.052577)1.000000:0.010070)1.000000:0.035671)1.000000:0.074417)1.000000:0.034385)1.000000:0.184380)1.000000:0.219467)1.000000:0.317782);'
nw_topo = '(Ddi0002240,Dme0014628,(Aga0007658,(Cin0011239,((Fru0004507,((Dre0008391,Dre0008390),Dre0008392)),((Xtr0044988,(Gga0000982,Gga0000981)),(Mdo0014718,((Mms0024821,Rno0030248),((Cfa0016700,Bta0018700),(Ptr0000001,((Hsa0010730,Hsa0000001),Hsa0010711))))))))));'
nw_dist = '(Ddi0002240:1.457468,Dme0014628:1.235133,(Aga0007658:1.752559,(Cin0011239:0.728210,((Fru0004507:0.184484,((Dre0008391:0.000000,Dre0008390:0.000000):0.002729,Dre0008392:0.010931):0.122420):0.142530,((Xtr0044988:0.422481,(Gga0000982:0.000000,Gga0000981:0.000000):0.109228):0.035488,(Mdo0014718:0.129337,((Mms0024821:0.027982,Rno0030248:0.029287):0.074667,((Cfa0016700:0.031643,Bta0018700:0.047366):0.007962,(Ptr0000001:0.005433,((Hsa0010730:0.018311,Hsa0000001:0.003656):0.007173,Hsa0010711:0.002730):0.014995):0.052577):0.010070):0.035671):0.074417):0.034385):0.184380):0.219467):0.317782);'
nw2_full = '((((((((YGR138C:0.038472,YPR156C:0.033397)1.000000:0.050097,YOR230W:0.220261)1.000000:0.114267,(YAL018C:0.035830,YBR287W:0.024912,YCL075W:0.030383,YDR055w:0.044474,YOR358W:0.045875)1.000000:0.030762)1.000000:0.061899,(YBR006W:0.012167,YBR241C:0.045848,YCR021c:0.011703,YCR061W:0.034785,YDL024c:0.030633,YDR298C:0.011081,YER141w:0.052598,YER158c:0.088493,YGR028W:0.015282,YGR149W:0.025905,YIR038C:0.021086,YJL155C:0.011531,YLR297W:0.052342,YLR423C:0.023426,YOL083W:0.046727,YOR049C:0.029090,YPL087W:0.015005)1.000000:0.010338)1.000000:0.022530,(YBR052C:0.044257,YBR054W:0.022772,YBR056W:0.033843,YBR183W:0.027453,YCL040w:0.076683,YCL042W:0.186523,YDL021W:0.007351,YDR032c:0.034443,YDR342C:0.024799,YDR343C:0.077931,YER053c:0.042805,YER150w:0.028763,YGR194C:0.019262,YGR244C:0.019371,YHR092C:0.064983,YIL111W:0.085602,YIR039C:0.061777,YJL079C:0.068661,YJL164C:0.066530,YJR073C:0.004770,YKL035W:0.114557,YMR250W:0.026205,YMR297W:0.057263,YNL160W:0.020050,YOR136W:0.031351,YOR273C:0.045478,YOR347C:0.017452,Ydr021w:0.029241,YPL154C:0.026716)1.000000:0.014156)1.000000:0.036360,((YBL078C:0.018348,YBR072W:0.008034,YBR139W:0.030263,YBR149W:0.017972,YBR169C:0.001920,YBR204C:0.017318,YDL022w:0.025509,YDL023c:0.042978,YDL091c:0.013934,YDR001C:0.014137,YDR077W:0.044424,YDR171W:0.011951,YDR178W:0.013526,YDR231C:0.005223,YDR258C:0.019661,YDR513W:0.016566,YDR529C:0.019541,YEL024w:0.020349,YFL014W:0.019925,YFR015C:0.027107,YFR033C:0.019186,YGL006W:0.019943,YGL187C:0.011290,YGL191W:0.030190,YGR008C:0.017479,YGR019W:0.017015,YGR088W:0.015580,YGR174C:0.011180,YHL021C:0.023666,YIL087C:0.011636,YIL107C:0.005697,YKL085W:0.003164,YKL103C:0.039112,YKL148C:0.022439,YKL150W?1:0.015616,YKR016W:0.017934,YKR067W:0.024008,YLL026w:0.019043,YLL041c:0.014446,YLR178C:0.029435,YLR258W:0.052186,YLR294C:0.024676,YLR299W:0.032933,YLR304C:0.045758,YLR327C:0.007435,YLR345W:0.005768,YLR395C:0.045549,YML100W:0.043110,YML120C:0.018385,YML128C:0.016054,YMR105C:0.024179,YMR110C:0.017258,YMR133W:0.023707,YMR196W:0.036526,YNL015W:0.019308,YNL055C:0.025667,YNL100W:0.004518,YNL144C:0.004901,YOL048C:0.026640,YOL053C:0.019814,YOR215C:0.010501,YOR317W:0.018442,YOR374W:0.011387,YPL078C:0.070312,YPL230W:0.020924,YPR149W:0.010801,YDR258C:0.014695)1.000000:0.008367,(YAL060W:0.015064,YBL038W:0.014364,YBL064C:0.028571,YBR269C:0.016747,YCL035C:0.025807,YDL004W:0.007085,YDR031w:0.003761,YDR074W:0.069217,YDR272W:0.011113,YDR272W:0.013582,YDR277C:0.032421,YDR516C:0.040793,YEL039c:0.016632,YER035w:0.024800,YER067w:0.038474,YER182w:0.011733,YFR053C:0.252371,YGL037C:0.047136,YGL121C:0.022573,YGL199C:0.011657,YGR248W:0.012191,YHR104W:0.015812,YIL113W:0.013517,YIL136W:0.039322,YIL162W:0.067884,YJL144W:0.022571,YJL151C:0.017277,YJR096W:0.019693,YKL026C:0.016814,YKL142W:0.033154,YKL151C:0.027220,YKL193C:0.017688,YLL023C:0.013887,YLR080W?1:0.010144,YLR270W:0.017368,YLR356W?1:0.007843,YML004C:0.047041,YMR030W:0.012315,YMR090W:0.048551,YMR170C:0.010852,YMR195W:0.035760,YNL045W:0.020669,YNL115C:0.048069,YNL173C:0.025198,YNL200C:0.026012,YNL274C:0.005603,YNL305C:0.034282,YNR073C:0.022308,YOL071W:0.026411,YOR052C:0.024637,YOR161C:0.021991,YOR220W:0.040045,YPL004C:0.024521)1.000000:0.013616)1.000000:0.006005)1.000000:0.021741,((((YAL034C:0.018415,YBL043W:0.024425,YBL049W:0.022513,YBR046C:0.031770,YCR039c:0.006232,YCR091w:0.026004,YDL079C:0.094125,YDL085w:0.032467,YDL204w:0.022855,YDL218w:0.016136,YDL223c:0.074370,YDR003W:0.073250,YDR018c:0.053591,YDR313C:0.025321,YIL097W:0.012089,YJL141C:0.035049,YKL093W:0.014752,YLR164W?1:0.011162,YLR168C:0.017070,YMR139W:0.035376,YNL093W:0.025831)1.000000:0.015975,((YBL048W:0.007604,YBL075C:0.014956,YBR067C:0.016580,YBR101C:0.007598,YBR147W:0.006150,YDR070c:0.010301,YGR236C:0.008648,YGR238C:0.010611,YGR243W:0.004473,YJL067W:0.007740,YKL016C:0.009956,YKL217W:0.009919,YLR216C:0.041156,YLR217W:0.018315,YLR219W:0.006671,YLR295C:0.017458,YMR107W:0.003236,YNL037C:0.011856,YNL134C:0.001122,YNL194C:0.003001,YNL202W:0.013719,YOR031W:0.014812)1.000000:0.006651,(YBR116C:0.033659,YDL020C:0.022419,YDR043C:0.056132,YDR262w:0.008193,YEL065w:0.266647,YGR146C:0.007376,YGR256W:0.035848,YJR155W:0.008535,YKL163W:0.036797,YNL036W:0.057108,YOR027W:0.016952,YPL135W:0.014251)1.000000:0.024637)1.000000:0.005255)1.000000:0.007999,(YOL109W:0.104113,YAL067C:0.023929,YBR053C:0.029405,YBR203W:0.013784,YBR214W:0.010883,YBR280C:0.017570,YDL169C:0.023945,YDL245C:0.040120,YDR148C:0.019495,YDR255C:0.031336,YDR329C:0.018032,YDR533C:0.001250,YER098w:0.018484,YER142c:0.030633,YER175c:0.004409,YGL045W:0.032391,YGL059W:0.050804,YGR043C:0.016315,YGR052W:0.044183,YGR066C:0.008994,YGR130C:0.022106,YGR201C:0.026083,YGR289C:0.013920,YHR195W:0.038417,YJL153C:0.033018,YJL161W:0.025820,YJR008W:0.027243,YJR080C:0.030356,YKR058W:0.010740,YLL001w:0.008319,YLR271W:0.028940,YMR271C:0.020724,YMR311C:0.031845,YMR322C:0.021606,YNR007C:0.020500,YOL032W:0.017985,YOL053W:0.040060,YOR178C:0.004028,YOR289W:0.017451,YOR386W:0.025749,YPL185W:0.017283,YPL186C:0.009140,YPR150W:0.025491)1.000000:0.011110)1.000000:0.012866,((YBL015W:0.018473,YBL099W:0.046953,YBL100C:0.046467,YBR039W:0.027280,YBR132C:0.057252,YDL181W:0.052427,YDR059C:0.028415,YDR085C:0.055567,YEL011w:0.020230,YER079w:0.013469,YFL030W:0.019404,YGL259W:0.019404,YGR070W:0.028021,YGR142W:0.002517,YGR250C:0.017097,YHL024W:0.016718,YHR051W:0.020669,YIL101C:0.040969,YJL103C:0.015318,YJR048W:0.013049,YJR121W:0.018256,YKL109W:0.013086,YKL141W:0.018280,YLR038c:0.046595,YLR149C:0.034217,YLR312C:0.025271,YML054C:0.014777,YMR031C:0.041817,YMR056C:0.024105,YMR081C:0.019086,YMR136W:0.078413,YMR181C:0.059683,YMR191W:0.007052,YNL052W:0.018461,YNR001C:0.008023,YOL117W:0.037811,YOL126C:0.058282,YOL153C:0.019880,YOR035C:0.045863,YOR065W:0.023359,YOR100C:0.021039,YPL165C:0.012048,YPL201C?1:0.009305,YPL223C:0.013347,YPR020W:0.014464,YPR098C:0.027269,YPR184W:0.035196)1.000000:0.007269,((YAL054C:0.010770,YDR125C:0.021905,YDR216W:0.027122,YEL012w:0.014583,YER024w:0.016562,YGL062W:0.266984,YIL125W:0.016436,YJL089W:0.010550,YJL163C:0.007033,YKL187C:0.012379,YLR259C:0.059779,YLR311C:0.011440,YNL009W:0.025277,YOL084W?1:0.005872,YPL262W:0.002576,YPR030W:0.011058)1.000000:0.010088,(YBL045C:0.015491,YBR001C:0.059987,YBR117C:0.033327,YBR298C:0.021627,YCR005c:0.008913,YDL199c:0.022880,YGL153W:0.006091,YGR110W:0.019326,YHL032C:0.008845,YHR096C:0.012855,YJL045W:0.007726,YJL137C:0.016000,YJR095W:0.035130,YKR076W:0.013664,YLR174W:0.025886,YLR267W:0.009587,YML042W:0.009641,YMR114C:0.242923,YMR206W:0.019201,YOR019W:0.035474,YOR391C:0.009738)1.000000:0.005262)1.000000:0.013775)1.000000:0.014916)1.000000:0.021186)1.000000:1.753931,((((((YCR054C:0.153934,YKL061W:0.133755,YLR109W:0.142228)1.000000:0.198112,(YBL054W:0.050037,YBR034C:0.038518,YGR177C:0.059524,YKL078W:0.026939,YKL106W:0.046488,YKR024C:0.035324,YLR380W:0.028761,YMR310C:0.034731,YOR271C:0.006213,YPL256C:0.059639)1.000000:0.012497)1.000000:0.065443,(YBR247C:0.050191,YBR267W:0.034203,YCLX02C:0.011558,YCR058C:0.051217,YDL151c:0.037685,YDR384C:0.011912,YDR465C:0.012999,YFL022C:0.009532,YGR159C:0.012299,YGR280C:0.013983,YHR206W:0.043975,YIL019W:0.086266,YIL065C:0.027422,YJL194W:0.096096,YKR056W:0.007362,YLL012W:0.031657,YLR073C:0.016216,YLR214W:0.039115,YLR293C:0.015673,YMR093W:0.009965,YMR259C:0.016481,YNR038W:0.015690,YOL019W:0.028424,YOL101C:0.023597,YOR272W:0.033415,YOR294W:0.033731,YPL043W:0.024688,YPL126W:0.011288,YPR144C:0.013358)1.000000:0.010101)1.000000:0.019870,((YBL068W:0.038979,YBR158W:0.008382,YBR186W:0.116086,YCR055C:0.061205,YCR065w:0.003695,YDL037c:0.048015,YDL042C:0.022897,YDL182w:0.039913,YDR508C:0.030289,YER145c:0.024536,YER165w:0.005328,YGR245C:0.009444,YJL069C:0.017205,YLR397C:0.033973,YMR108W:0.024272,YMR309C:0.017863,YNL124W:0.016342,YNL189W:0.033389,YOL007C:0.062976,YOL130W?1:0.068678)1.000000:0.017449,((YAL043C:0.085408,YDR006C:0.131879,YHR205W:0.038850,YJL195C:0.040006,YPL061W:0.070549)1.000000:0.031474,(YDR101C:0.068051,YKL185W:0.029377,YNL061W:0.047111,YOR091W:0.057478)1.000000:0.047015)1.000000:0.102596)1.000000:0.046055)1.000000:0.039969,(YAL003W:0.027682,YAL025C:0.008438,YAL046C:0.016620,YAL059W:0.051270,YAR071W:0.027037,YAR074C:0.005698,YBL024W:0.008170,YBL039C:0.039903,YBR069C:0.243928,YBR079C:0.025916,YBR089W:0.031468,YBR093C:0.043355,YBR142W:0.051410,YBR238C:0.051070,YBR266C:0.043018,YCL046W:0.019256,YCL054W:0.041245,YCR053w:0.025386,YDL050c:0.008063,YDL051W:0.022365,YDL052C:0.053016,YDL063c:0.018176,YDL084w:0.016863,YDL111c:0.008781,YDL122W:0.043325,YDL131w:0.108001,YDL140C:0.024567,YDL148c:0.046571,YDL152w:0.055074,YDL153c:0.017418,YDL167C:0.009333,YDL213c:0.017884,YDR024w:0.148026,YDR144C:0.010083,YDR165W:0.015923,YDR206W:0.005912,YDR324C:0.042943,YDR341C:0.015004,YDR361C:0.015177,YDR398W:0.018739,YDR492W:0.019353,YDR502C:0.023435,YDR527W:0.025343,YEL033w:0.020575,YEL040w:0.048325,YEL046c:0.015069,YER002w:0.014535,YER006w:0.017578,YER025w:0.014587,YER036c:0.016587,YER043c:0.030110,YER049w:0.045735,YER052c:0.022026,YER070w:0.021812,YER110c:0.022076,YGR103W:0.034426,YGR123C:0.049640,YGR124W:0.006737,YGR145W:0.025280,YGR155W:0.054731,YGR160W:0.013018,YGR162W:0.020365,YGR264C:0.018057,YHR046C:0.180512,YHR052W:0.010195,YHR064C:0.016477,YHR070W:0.036840,YHR215W:0.030425,YIL053W:0.012927,YIL066C:0.008671,YIL091C:0.003393,YJL050W:0.016488,YJL109C:0.060257,YJL122W:0.017642,YJR003C:0.022002,YJR016C:0.014266,YJR041C:0.020306,YJR054W:0.037849,YKL076C:0.038156,YKL082C:0.012586,YKL181W:0.005029,YKL191W:0.099536,YLL008w:0.016875,YLL021w:0.024558,YLR068W:0.079458,YLR084C:0.035147,YLR180W:0.009062,YLR196W:0.046001,YLR221C:0.028516,YLR223C:0.057444,YLR243W:0.010906,YLR244C:0.037764,YLR280C:0.020274,YLR355C:0.025286,YLR409C:0.009258,YLR435W:0.092123,YLR449W:0.018710,YML123C:0.018546,YMR011W:0.032472,YMR014W:0.007539,YMR037C:0.063027,YMR049C:0.011294,YMR058W:0.010664,YMR080C:0.040422,YMR128W:0.033444,YMR129W:0.046421,YMR146C:0.021802,YMR217W:0.041486,YMR229C:0.004043,YMR239C:0.006788,YMR241W:0.012776,YMR246W:0.023201,YMR290C:0.003882,YNL002C:0.029441,YNL013C:0.037125,YNL060C:0.001669,YNL062C:0.014338,YNL075W:0.012303,YNL110C:0.007903,YNL112W:0.034459,YNL120C:0.018624,YNL123W:0.022098,YNL132W:0.003370,YNL141W:0.009783,YNL174W:0.101658,YNL182C:0.007662,YNL207W:0.014884,YNL216W:0.170324,YNL221C:0.015522,YNL256W:0.011304,YNL308C:0.045905,YNL313C:0.026778,YNL327W:0.008828,YNR025C:0.048977,YNR043W:0.020504,YNR046W:0.055271,YNR054C:0.005370,YNR075W:0.013830,YOL021C:0.010752,YOL080C:0.031182,YOR116C:0.029862,YOR146W:0.053670,YOR206W:0.051387,YOR233W:0.036870,YOR335C:0.009945,YOR341W:0.023363,YOR355W:0.015312,YOR361C:0.022609,YPL012W:0.003133,YPL019C:0.014463,YPL030W:0.011898,YPL032C:0.047324,YPL093W:0.009715,YPL183C:0.087818,YPL211W:0.006930,YPL226W:0.013388,YPR009W:0.025512,YPR034W:0.010374,YPR110C:0.009930,YPR136C:0.133899,YPR143W:0.021514,YPR145W:0.025839)1.000000:0.005840)1.000000:0.024107,((YHR007C:0.024321,YAL023C:0.037896,YAL036C:0.027457,YAR073W:0.007629,YBL076C:0.007966,YBL087C:0.016367,YBR048W:0.037560,YBR092C:0.027230,YBR121C:0.027699,YBR143C:0.022332,YBR156C:0.004017,YBR249C:0.000577,YCL053C:0.012758,YDL014W:0.011777,YDL060w:0.008162,YDL082w:0.006478,YDL145C:0.025230,YDL208W:0.003093,YDR023W:0.039428,YDR037W:0.023439,YDR060w:0.005655,YDR062W:0.013960,YDR064W:0.002168,YDR321W:0.006361,YDR365C:0.006326,YDR399W:0.003641,YDR447C:0.015148,YDR449C:0.001937,YDR450W:0.016031,YDR471W:0.015488,YEL026w:0.019446,YEL054c:0.008555,YER056c:0.022337,YER060w:0.036023,YER129w:0.011346,YFL045C:0.053502,YGL008C:0.012515,YGL029W:0.067475,YGL078C:0.045179,YGL092W:0.045425,YGL103W:0.009550,YGL225W:0.027201,YGR034W:0.012058,YGR060W:0.013105,YGR061C:0.009325,YGR214W:0.007962,YHL033C:0.014192,YHR019C:0.019476,YHR049W:0.036925,YHR089C:0.010167,YHR128W:0.008165,YHR203C:0.007600,YHR216W:0.002384,YIL052C:0.013691,YIL069C:0.012335,YIL133C:0.004129,YJL111W:0.017878,YJL138C:0.009234,YJL177W:0.002417,YJL183W:0.005059,YJR071W:0.008702,YJR105W:0.058597,YJR123W:0.003913,YKL009W:0.009543,YKL057C:0.034921,YKL081W:0.007191,YKL156W:0.011042,YKR013W:0.029496,YKR025W:0.021172,YKR094C:0.008062,YLL004w:0.026716,YLL044W:0.008058,YLR009W:0.012315,YLR048w:0.004366,YLR056w:0.028151,YLR061W:0.003944,YLR083c:0.016167,YLR129w:0.052379,YLR134w:0.018072,YLR175W:0.025815,YLR179C:0.014679,YLR185W:0.007868,YLR186W:0.055986,YLR212C:0.006866,YLR339C:0.013427,YLR384C:0.043396,YLR413W:0.007107,YLR432W:0.000390,YLR448W:0.013913,YML059C:0.068679,YMR199W:0.180049,YMR202W:0.013830,YMR205C:0.011290,YMR242C:0.002943,YMR308C:0.012121,YMR318C:0.009922,YMR321C:0.007602,YNL065W:0.040820,YNL087W:0.011444,YNL096C:0.016268,YNL111C:0.009092,YNL175C:0.021305,YNL235C:0.017678,YNL247W:0.010779,YNL301C:0.006244,YNL303W:0.026882,YNR009W:0.069305,YNR051C:0.005803,YNR053C:0.011495,YNR067C:0.038533,YOL010W:0.013445,YOL014W:0.050775,YOL120C:0.011740,YOL061W:0.014505,YOL077C:0.027831,YOR063W:0.004912,YOR096W:0.009238,YOR153W:0.010446,YOR234C:0.008998,YOR277C:0.023939,YOR293W:0.013614,YOR309C:0.007759,YPL034W:0.035088,YPL143W:0.030537,YPL160W:0.018401,YPL198W:0.002841,YPL243W:0.014395,YPL245W:0.004341,YPL266W:0.015510,YPR033C:0.028234,YPR044C:0.016689,YPR074C:0.006226,YPR112C:0.012512,YPR125W:0.030210,YHR098C:0.005812)1.000000:0.005387,((YAL012W:0.037345,YAL038W:0.007617,YBL027W:0.013554,YBR106W:0.006914,YBR189W:0.010072,YBR191W:0.005150,YDL075W:0.007897,YDL083C:0.031836,YDL136w:0.006651,YDL191W:0.011001,YDL210W:0.015110,YDR366C:0.015185,YDR417C:0.003784,YDR418W:0.001455,YDR500C:0.007442,YER074w:0.008117,YER117w:0.008649,YER131w:0.002672,YFR031BC:0.012496,YGL030W:0.003864,YGL076C:0.013045,YGL123W:0.012111,YGL135W:0.018213,YGL147C:0.004678,YGR118W:0.013782,YGR148C:0.005154,YGR285C:0.024308,YHL001W:0.021713,YHL015W:0.009606,YHR010W:0.002032,YHR141C:0.007074,YHR208W:0.038459,YIL018W:0.000289,YIL039W:0.015756,YIL148W:0.016059,YJL080C:0.017726,YJL136C:0.009858,YJL148W:0.025592,YJL188C?1:0.009377,YJL189W:0.030581,YJR063W:0.036817,YJR145C:0.011576,YKL006W:0.005959,YKR043C:0.016532,YKR057W:0.009924,YKR059W:0.011284,YLL045c:0.014089,YLL047W:0.023354,YLR029c:0.010768,YLR044c:0.011219,YLR060w:0.020979,YLR062C:0.006945,YLR076C:0.010549,YLR198C:0.003174,YLR249W:0.022251,YLR325C:0.009715,YLR340W:0.008365,YLR344W:0.010317,YLR367W:0.003094,YLR388W:0.021736,YML063W:0.006051,YMR121C:0.017411,YMR131C:0.026306,YNL119W:0.014916,YNL162W:0.016264,YNL302C:0.004123,YNR050C:0.058206,YOL121C:0.009887,YOL127W:0.013974,YOL040C:0.007057,YOR224C:0.013626,YOR254C:0.017923,YOR310C:0.006634,YOR312C:0.003510,YPL079W:0.030247,YPL131W:0.022146,YPL142C:0.015716,YPL220W:0.009552,YPL244C:0.022966,YPR102C:0.008204,YPR137W:0.017679)1.000000:0.002907,((YBR032W:0.016097,YBR181C:0.009522,YBR187W:0.018681,YDR012W:0.011279,YGL102C:0.009205,YGR027C:0.003690,YJL157C:0.024018,YJL190C:0.007303,YLR058c:0.073551,YLR264W:0.018569,YLR300W:0.020115,YLR342W:0.034792,YLR359W:0.022991,YLR372W:0.011058,YMR300C:0.032100,YMR305C:0.014402,YNL069C:0.028621,YOR133W:0.004537,YOR167C:0.014198,YOR182C:0.023853,YOR326W:0.024632,YPL080C:0.064427,YPL081W:0.012279,YPL090C:0.012152)1.000000:0.006473,(YOR298W:0.233587,((YDR019C:0.040149,YKL096W:0.037806)1.000000:0.064948,(YKL108W:0.033111,YPR113W:0.038607)1.000000:0.063282)1.000000:0.016535)1.000000:0.229462)1.000000:0.024472)1.000000:0.008239)1.000000:0.017711)1.000000:0.082401);'
nw_full = '(Ddi0002240:1.45747,Dme0014628:1.23513,(Aga0007658:1.75256,(Cin0011239:0.72821,((Fru0004507:0.184484,((Dre0008391:0,Dre0008390:0)1:0.002729,Dre0008392:0.010931)1:0.12242)1:0.14253,((Xtr0044988:0.422481,(Gga0000982:0,Gga0000981:0)1:0.109228)1:0.035488,(Mdo0014718:0.129337,((Mms0024821:0.027982,Rno0030248:0.029287)1:0.074667,((Cfa0016700:0.031643,Bta0018700:0.047366)1:0.007962,(Ptr0000001:0.005433,((Hsa0010730:0.018311[&&NHX:flag=Red],Hsa0000001:0.003656)1:0.007173,Hsa0010711:0.00273)1:0.014995)1:0.052577)1:0.01007)1:0.035671)1:0.074417)1:0.034385)1:0.18438[&&NHX:flag=Black])1:0.219467)1:0.317782[&&NHX:flag=White]);'
nw_dflt = '(Ddi0002240:1.45747,Dme0014628:1.23513,(Aga0007658:1.75256,(Cin0011239:0.72821,((Fru0004507:0.184484,((Dre0008391:0,Dre0008390:0)1:0.002729,Dre0008392:0.010931)1:0.12242)1:0.14253,((Xtr0044988:0.422481,(Gga0000982:0,Gga0000981:0)1:0.109228)1:0.035488,(Mdo0014718:0.129337,((Mms0024821:0.027982,Rno0030248:0.029287)1:0.074667,((Cfa0016700:0.031643,Bta0018700:0.047366)1:0.007962,(Ptr0000001:0.005433,((Hsa0010730:0.018311,Hsa0000001:0.003656)1:0.007173,Hsa0010711:0.00273)1:0.014995)1:0.052577)1:0.01007)1:0.035671)1:0.074417)1:0.034385)1:0.18438)1:0.219467)1:0.317782);'
nw_topo = '(Ddi0002240,Dme0014628,(Aga0007658,(Cin0011239,((Fru0004507,((Dre0008391,Dre0008390),Dre0008392)),((Xtr0044988,(Gga0000982,Gga0000981)),(Mdo0014718,((Mms0024821,Rno0030248),((Cfa0016700,Bta0018700),(Ptr0000001,((Hsa0010730,Hsa0000001),Hsa0010711))))))))));'
nw_dist = '(Ddi0002240:1.45747,Dme0014628:1.23513,(Aga0007658:1.75256,(Cin0011239:0.72821,((Fru0004507:0.184484,((Dre0008391:0,Dre0008390:0):0.002729,Dre0008392:0.010931):0.12242):0.14253,((Xtr0044988:0.422481,(Gga0000982:0,Gga0000981:0):0.109228):0.035488,(Mdo0014718:0.129337,((Mms0024821:0.027982,Rno0030248:0.029287):0.074667,((Cfa0016700:0.031643,Bta0018700:0.047366):0.007962,(Ptr0000001:0.005433,((Hsa0010730:0.018311,Hsa0000001:0.003656):0.007173,Hsa0010711:0.00273):0.014995):0.052577):0.01007):0.035671):0.074417):0.034385):0.18438):0.219467):0.317782);'
nw2_full = '((((((((YGR138C:0.038472,YPR156C:0.033397)1:0.050097,YOR230W:0.220261)1:0.114267,(YAL018C:0.03583,YBR287W:0.024912,YCL075W:0.030383,YDR055w:0.044474,YOR358W:0.045875)1:0.030762)1:0.061899,(YBR006W:0.012167,YBR241C:0.045848,YCR021c:0.011703,YCR061W:0.034785,YDL024c:0.030633,YDR298C:0.011081,YER141w:0.052598,YER158c:0.088493,YGR028W:0.015282,YGR149W:0.025905,YIR038C:0.021086,YJL155C:0.011531,YLR297W:0.052342,YLR423C:0.023426,YOL083W:0.046727,YOR049C:0.02909,YPL087W:0.015005)1:0.010338)1:0.02253,(YBR052C:0.044257,YBR054W:0.022772,YBR056W:0.033843,YBR183W:0.027453,YCL040w:0.076683,YCL042W:0.186523,YDL021W:0.007351,YDR032c:0.034443,YDR342C:0.024799,YDR343C:0.077931,YER053c:0.042805,YER150w:0.028763,YGR194C:0.019262,YGR244C:0.019371,YHR092C:0.064983,YIL111W:0.085602,YIR039C:0.061777,YJL079C:0.068661,YJL164C:0.06653,YJR073C:0.00477,YKL035W:0.114557,YMR250W:0.026205,YMR297W:0.057263,YNL160W:0.02005,YOR136W:0.031351,YOR273C:0.045478,YOR347C:0.017452,Ydr021w:0.029241,YPL154C:0.026716)1:0.014156)1:0.03636,((YBL078C:0.018348,YBR072W:0.008034,YBR139W:0.030263,YBR149W:0.017972,YBR169C:0.00192,YBR204C:0.017318,YDL022w:0.025509,YDL023c:0.042978,YDL091c:0.013934,YDR001C:0.014137,YDR077W:0.044424,YDR171W:0.011951,YDR178W:0.013526,YDR231C:0.005223,YDR258C:0.019661,YDR513W:0.016566,YDR529C:0.019541,YEL024w:0.020349,YFL014W:0.019925,YFR015C:0.027107,YFR033C:0.019186,YGL006W:0.019943,YGL187C:0.01129,YGL191W:0.03019,YGR008C:0.017479,YGR019W:0.017015,YGR088W:0.01558,YGR174C:0.01118,YHL021C:0.023666,YIL087C:0.011636,YIL107C:0.005697,YKL085W:0.003164,YKL103C:0.039112,YKL148C:0.022439,YKL150W?1:0.015616,YKR016W:0.017934,YKR067W:0.024008,YLL026w:0.019043,YLL041c:0.014446,YLR178C:0.029435,YLR258W:0.052186,YLR294C:0.024676,YLR299W:0.032933,YLR304C:0.045758,YLR327C:0.007435,YLR345W:0.005768,YLR395C:0.045549,YML100W:0.04311,YML120C:0.018385,YML128C:0.016054,YMR105C:0.024179,YMR110C:0.017258,YMR133W:0.023707,YMR196W:0.036526,YNL015W:0.019308,YNL055C:0.025667,YNL100W:0.004518,YNL144C:0.004901,YOL048C:0.02664,YOL053C:0.019814,YOR215C:0.010501,YOR317W:0.018442,YOR374W:0.011387,YPL078C:0.070312,YPL230W:0.020924,YPR149W:0.010801,YDR258C:0.014695)1:0.008367,(YAL060W:0.015064,YBL038W:0.014364,YBL064C:0.028571,YBR269C:0.016747,YCL035C:0.025807,YDL004W:0.007085,YDR031w:0.003761,YDR074W:0.069217,YDR272W:0.011113,YDR272W:0.013582,YDR277C:0.032421,YDR516C:0.040793,YEL039c:0.016632,YER035w:0.0248,YER067w:0.038474,YER182w:0.011733,YFR053C:0.252371,YGL037C:0.047136,YGL121C:0.022573,YGL199C:0.011657,YGR248W:0.012191,YHR104W:0.015812,YIL113W:0.013517,YIL136W:0.039322,YIL162W:0.067884,YJL144W:0.022571,YJL151C:0.017277,YJR096W:0.019693,YKL026C:0.016814,YKL142W:0.033154,YKL151C:0.02722,YKL193C:0.017688,YLL023C:0.013887,YLR080W?1:0.010144,YLR270W:0.017368,YLR356W?1:0.007843,YML004C:0.047041,YMR030W:0.012315,YMR090W:0.048551,YMR170C:0.010852,YMR195W:0.03576,YNL045W:0.020669,YNL115C:0.048069,YNL173C:0.025198,YNL200C:0.026012,YNL274C:0.005603,YNL305C:0.034282,YNR073C:0.022308,YOL071W:0.026411,YOR052C:0.024637,YOR161C:0.021991,YOR220W:0.040045,YPL004C:0.024521)1:0.013616)1:0.006005)1:0.021741,((((YAL034C:0.018415,YBL043W:0.024425,YBL049W:0.022513,YBR046C:0.03177,YCR039c:0.006232,YCR091w:0.026004,YDL079C:0.094125,YDL085w:0.032467,YDL204w:0.022855,YDL218w:0.016136,YDL223c:0.07437,YDR003W:0.07325,YDR018c:0.053591,YDR313C:0.025321,YIL097W:0.012089,YJL141C:0.035049,YKL093W:0.014752,YLR164W?1:0.011162,YLR168C:0.01707,YMR139W:0.035376,YNL093W:0.025831)1:0.015975,((YBL048W:0.007604,YBL075C:0.014956,YBR067C:0.01658,YBR101C:0.007598,YBR147W:0.00615,YDR070c:0.010301,YGR236C:0.008648,YGR238C:0.010611,YGR243W:0.004473,YJL067W:0.00774,YKL016C:0.009956,YKL217W:0.009919,YLR216C:0.041156,YLR217W:0.018315,YLR219W:0.006671,YLR295C:0.017458,YMR107W:0.003236,YNL037C:0.011856,YNL134C:0.001122,YNL194C:0.003001,YNL202W:0.013719,YOR031W:0.014812)1:0.006651,(YBR116C:0.033659,YDL020C:0.022419,YDR043C:0.056132,YDR262w:0.008193,YEL065w:0.266647,YGR146C:0.007376,YGR256W:0.035848,YJR155W:0.008535,YKL163W:0.036797,YNL036W:0.057108,YOR027W:0.016952,YPL135W:0.014251)1:0.024637)1:0.005255)1:0.007999,(YOL109W:0.104113,YAL067C:0.023929,YBR053C:0.029405,YBR203W:0.013784,YBR214W:0.010883,YBR280C:0.01757,YDL169C:0.023945,YDL245C:0.04012,YDR148C:0.019495,YDR255C:0.031336,YDR329C:0.018032,YDR533C:0.00125,YER098w:0.018484,YER142c:0.030633,YER175c:0.004409,YGL045W:0.032391,YGL059W:0.050804,YGR043C:0.016315,YGR052W:0.044183,YGR066C:0.008994,YGR130C:0.022106,YGR201C:0.026083,YGR289C:0.01392,YHR195W:0.038417,YJL153C:0.033018,YJL161W:0.02582,YJR008W:0.027243,YJR080C:0.030356,YKR058W:0.01074,YLL001w:0.008319,YLR271W:0.02894,YMR271C:0.020724,YMR311C:0.031845,YMR322C:0.021606,YNR007C:0.0205,YOL032W:0.017985,YOL053W:0.04006,YOR178C:0.004028,YOR289W:0.017451,YOR386W:0.025749,YPL185W:0.017283,YPL186C:0.00914,YPR150W:0.025491)1:0.01111)1:0.012866,((YBL015W:0.018473,YBL099W:0.046953,YBL100C:0.046467,YBR039W:0.02728,YBR132C:0.057252,YDL181W:0.052427,YDR059C:0.028415,YDR085C:0.055567,YEL011w:0.02023,YER079w:0.013469,YFL030W:0.019404,YGL259W:0.019404,YGR070W:0.028021,YGR142W:0.002517,YGR250C:0.017097,YHL024W:0.016718,YHR051W:0.020669,YIL101C:0.040969,YJL103C:0.015318,YJR048W:0.013049,YJR121W:0.018256,YKL109W:0.013086,YKL141W:0.01828,YLR038c:0.046595,YLR149C:0.034217,YLR312C:0.025271,YML054C:0.014777,YMR031C:0.041817,YMR056C:0.024105,YMR081C:0.019086,YMR136W:0.078413,YMR181C:0.059683,YMR191W:0.007052,YNL052W:0.018461,YNR001C:0.008023,YOL117W:0.037811,YOL126C:0.058282,YOL153C:0.01988,YOR035C:0.045863,YOR065W:0.023359,YOR100C:0.021039,YPL165C:0.012048,YPL201C?1:0.009305,YPL223C:0.013347,YPR020W:0.014464,YPR098C:0.027269,YPR184W:0.035196)1:0.007269,((YAL054C:0.01077,YDR125C:0.021905,YDR216W:0.027122,YEL012w:0.014583,YER024w:0.016562,YGL062W:0.266984,YIL125W:0.016436,YJL089W:0.01055,YJL163C:0.007033,YKL187C:0.012379,YLR259C:0.059779,YLR311C:0.01144,YNL009W:0.025277,YOL084W?1:0.005872,YPL262W:0.002576,YPR030W:0.011058)1:0.010088,(YBL045C:0.015491,YBR001C:0.059987,YBR117C:0.033327,YBR298C:0.021627,YCR005c:0.008913,YDL199c:0.02288,YGL153W:0.006091,YGR110W:0.019326,YHL032C:0.008845,YHR096C:0.012855,YJL045W:0.007726,YJL137C:0.016,YJR095W:0.03513,YKR076W:0.013664,YLR174W:0.025886,YLR267W:0.009587,YML042W:0.009641,YMR114C:0.242923,YMR206W:0.019201,YOR019W:0.035474,YOR391C:0.009738)1:0.005262)1:0.013775)1:0.014916)1:0.021186)1:1.75393,((((((YCR054C:0.153934,YKL061W:0.133755,YLR109W:0.142228)1:0.198112,(YBL054W:0.050037,YBR034C:0.038518,YGR177C:0.059524,YKL078W:0.026939,YKL106W:0.046488,YKR024C:0.035324,YLR380W:0.028761,YMR310C:0.034731,YOR271C:0.006213,YPL256C:0.059639)1:0.012497)1:0.065443,(YBR247C:0.050191,YBR267W:0.034203,YCLX02C:0.011558,YCR058C:0.051217,YDL151c:0.037685,YDR384C:0.011912,YDR465C:0.012999,YFL022C:0.009532,YGR159C:0.012299,YGR280C:0.013983,YHR206W:0.043975,YIL019W:0.086266,YIL065C:0.027422,YJL194W:0.096096,YKR056W:0.007362,YLL012W:0.031657,YLR073C:0.016216,YLR214W:0.039115,YLR293C:0.015673,YMR093W:0.009965,YMR259C:0.016481,YNR038W:0.01569,YOL019W:0.028424,YOL101C:0.023597,YOR272W:0.033415,YOR294W:0.033731,YPL043W:0.024688,YPL126W:0.011288,YPR144C:0.013358)1:0.010101)1:0.01987,((YBL068W:0.038979,YBR158W:0.008382,YBR186W:0.116086,YCR055C:0.061205,YCR065w:0.003695,YDL037c:0.048015,YDL042C:0.022897,YDL182w:0.039913,YDR508C:0.030289,YER145c:0.024536,YER165w:0.005328,YGR245C:0.009444,YJL069C:0.017205,YLR397C:0.033973,YMR108W:0.024272,YMR309C:0.017863,YNL124W:0.016342,YNL189W:0.033389,YOL007C:0.062976,YOL130W?1:0.068678)1:0.017449,((YAL043C:0.085408,YDR006C:0.131879,YHR205W:0.03885,YJL195C:0.040006,YPL061W:0.070549)1:0.031474,(YDR101C:0.068051,YKL185W:0.029377,YNL061W:0.047111,YOR091W:0.057478)1:0.047015)1:0.102596)1:0.046055)1:0.039969,(YAL003W:0.027682,YAL025C:0.008438,YAL046C:0.01662,YAL059W:0.05127,YAR071W:0.027037,YAR074C:0.005698,YBL024W:0.00817,YBL039C:0.039903,YBR069C:0.243928,YBR079C:0.025916,YBR089W:0.031468,YBR093C:0.043355,YBR142W:0.05141,YBR238C:0.05107,YBR266C:0.043018,YCL046W:0.019256,YCL054W:0.041245,YCR053w:0.025386,YDL050c:0.008063,YDL051W:0.022365,YDL052C:0.053016,YDL063c:0.018176,YDL084w:0.016863,YDL111c:0.008781,YDL122W:0.043325,YDL131w:0.108001,YDL140C:0.024567,YDL148c:0.046571,YDL152w:0.055074,YDL153c:0.017418,YDL167C:0.009333,YDL213c:0.017884,YDR024w:0.148026,YDR144C:0.010083,YDR165W:0.015923,YDR206W:0.005912,YDR324C:0.042943,YDR341C:0.015004,YDR361C:0.015177,YDR398W:0.018739,YDR492W:0.019353,YDR502C:0.023435,YDR527W:0.025343,YEL033w:0.020575,YEL040w:0.048325,YEL046c:0.015069,YER002w:0.014535,YER006w:0.017578,YER025w:0.014587,YER036c:0.016587,YER043c:0.03011,YER049w:0.045735,YER052c:0.022026,YER070w:0.021812,YER110c:0.022076,YGR103W:0.034426,YGR123C:0.04964,YGR124W:0.006737,YGR145W:0.02528,YGR155W:0.054731,YGR160W:0.013018,YGR162W:0.020365,YGR264C:0.018057,YHR046C:0.180512,YHR052W:0.010195,YHR064C:0.016477,YHR070W:0.03684,YHR215W:0.030425,YIL053W:0.012927,YIL066C:0.008671,YIL091C:0.003393,YJL050W:0.016488,YJL109C:0.060257,YJL122W:0.017642,YJR003C:0.022002,YJR016C:0.014266,YJR041C:0.020306,YJR054W:0.037849,YKL076C:0.038156,YKL082C:0.012586,YKL181W:0.005029,YKL191W:0.099536,YLL008w:0.016875,YLL021w:0.024558,YLR068W:0.079458,YLR084C:0.035147,YLR180W:0.009062,YLR196W:0.046001,YLR221C:0.028516,YLR223C:0.057444,YLR243W:0.010906,YLR244C:0.037764,YLR280C:0.020274,YLR355C:0.025286,YLR409C:0.009258,YLR435W:0.092123,YLR449W:0.01871,YML123C:0.018546,YMR011W:0.032472,YMR014W:0.007539,YMR037C:0.063027,YMR049C:0.011294,YMR058W:0.010664,YMR080C:0.040422,YMR128W:0.033444,YMR129W:0.046421,YMR146C:0.021802,YMR217W:0.041486,YMR229C:0.004043,YMR239C:0.006788,YMR241W:0.012776,YMR246W:0.023201,YMR290C:0.003882,YNL002C:0.029441,YNL013C:0.037125,YNL060C:0.001669,YNL062C:0.014338,YNL075W:0.012303,YNL110C:0.007903,YNL112W:0.034459,YNL120C:0.018624,YNL123W:0.022098,YNL132W:0.00337,YNL141W:0.009783,YNL174W:0.101658,YNL182C:0.007662,YNL207W:0.014884,YNL216W:0.170324,YNL221C:0.015522,YNL256W:0.011304,YNL308C:0.045905,YNL313C:0.026778,YNL327W:0.008828,YNR025C:0.048977,YNR043W:0.020504,YNR046W:0.055271,YNR054C:0.00537,YNR075W:0.01383,YOL021C:0.010752,YOL080C:0.031182,YOR116C:0.029862,YOR146W:0.05367,YOR206W:0.051387,YOR233W:0.03687,YOR335C:0.009945,YOR341W:0.023363,YOR355W:0.015312,YOR361C:0.022609,YPL012W:0.003133,YPL019C:0.014463,YPL030W:0.011898,YPL032C:0.047324,YPL093W:0.009715,YPL183C:0.087818,YPL211W:0.00693,YPL226W:0.013388,YPR009W:0.025512,YPR034W:0.010374,YPR110C:0.00993,YPR136C:0.133899,YPR143W:0.021514,YPR145W:0.025839)1:0.00584)1:0.024107,((YHR007C:0.024321,YAL023C:0.037896,YAL036C:0.027457,YAR073W:0.007629,YBL076C:0.007966,YBL087C:0.016367,YBR048W:0.03756,YBR092C:0.02723,YBR121C:0.027699,YBR143C:0.022332,YBR156C:0.004017,YBR249C:0.000577,YCL053C:0.012758,YDL014W:0.011777,YDL060w:0.008162,YDL082w:0.006478,YDL145C:0.02523,YDL208W:0.003093,YDR023W:0.039428,YDR037W:0.023439,YDR060w:0.005655,YDR062W:0.01396,YDR064W:0.002168,YDR321W:0.006361,YDR365C:0.006326,YDR399W:0.003641,YDR447C:0.015148,YDR449C:0.001937,YDR450W:0.016031,YDR471W:0.015488,YEL026w:0.019446,YEL054c:0.008555,YER056c:0.022337,YER060w:0.036023,YER129w:0.011346,YFL045C:0.053502,YGL008C:0.012515,YGL029W:0.067475,YGL078C:0.045179,YGL092W:0.045425,YGL103W:0.00955,YGL225W:0.027201,YGR034W:0.012058,YGR060W:0.013105,YGR061C:0.009325,YGR214W:0.007962,YHL033C:0.014192,YHR019C:0.019476,YHR049W:0.036925,YHR089C:0.010167,YHR128W:0.008165,YHR203C:0.0076,YHR216W:0.002384,YIL052C:0.013691,YIL069C:0.012335,YIL133C:0.004129,YJL111W:0.017878,YJL138C:0.009234,YJL177W:0.002417,YJL183W:0.005059,YJR071W:0.008702,YJR105W:0.058597,YJR123W:0.003913,YKL009W:0.009543,YKL057C:0.034921,YKL081W:0.007191,YKL156W:0.011042,YKR013W:0.029496,YKR025W:0.021172,YKR094C:0.008062,YLL004w:0.026716,YLL044W:0.008058,YLR009W:0.012315,YLR048w:0.004366,YLR056w:0.028151,YLR061W:0.003944,YLR083c:0.016167,YLR129w:0.052379,YLR134w:0.018072,YLR175W:0.025815,YLR179C:0.014679,YLR185W:0.007868,YLR186W:0.055986,YLR212C:0.006866,YLR339C:0.013427,YLR384C:0.043396,YLR413W:0.007107,YLR432W:0.00039,YLR448W:0.013913,YML059C:0.068679,YMR199W:0.180049,YMR202W:0.01383,YMR205C:0.01129,YMR242C:0.002943,YMR308C:0.012121,YMR318C:0.009922,YMR321C:0.007602,YNL065W:0.04082,YNL087W:0.011444,YNL096C:0.016268,YNL111C:0.009092,YNL175C:0.021305,YNL235C:0.017678,YNL247W:0.010779,YNL301C:0.006244,YNL303W:0.026882,YNR009W:0.069305,YNR051C:0.005803,YNR053C:0.011495,YNR067C:0.038533,YOL010W:0.013445,YOL014W:0.050775,YOL120C:0.01174,YOL061W:0.014505,YOL077C:0.027831,YOR063W:0.004912,YOR096W:0.009238,YOR153W:0.010446,YOR234C:0.008998,YOR277C:0.023939,YOR293W:0.013614,YOR309C:0.007759,YPL034W:0.035088,YPL143W:0.030537,YPL160W:0.018401,YPL198W:0.002841,YPL243W:0.014395,YPL245W:0.004341,YPL266W:0.01551,YPR033C:0.028234,YPR044C:0.016689,YPR074C:0.006226,YPR112C:0.012512,YPR125W:0.03021,YHR098C:0.005812)1:0.005387,((YAL012W:0.037345,YAL038W:0.007617,YBL027W:0.013554,YBR106W:0.006914,YBR189W:0.010072,YBR191W:0.00515,YDL075W:0.007897,YDL083C:0.031836,YDL136w:0.006651,YDL191W:0.011001,YDL210W:0.01511,YDR366C:0.015185,YDR417C:0.003784,YDR418W:0.001455,YDR500C:0.007442,YER074w:0.008117,YER117w:0.008649,YER131w:0.002672,YFR031BC:0.012496,YGL030W:0.003864,YGL076C:0.013045,YGL123W:0.012111,YGL135W:0.018213,YGL147C:0.004678,YGR118W:0.013782,YGR148C:0.005154,YGR285C:0.024308,YHL001W:0.021713,YHL015W:0.009606,YHR010W:0.002032,YHR141C:0.007074,YHR208W:0.038459,YIL018W:0.000289,YIL039W:0.015756,YIL148W:0.016059,YJL080C:0.017726,YJL136C:0.009858,YJL148W:0.025592,YJL188C?1:0.009377,YJL189W:0.030581,YJR063W:0.036817,YJR145C:0.011576,YKL006W:0.005959,YKR043C:0.016532,YKR057W:0.009924,YKR059W:0.011284,YLL045c:0.014089,YLL047W:0.023354,YLR029c:0.010768,YLR044c:0.011219,YLR060w:0.020979,YLR062C:0.006945,YLR076C:0.010549,YLR198C:0.003174,YLR249W:0.022251,YLR325C:0.009715,YLR340W:0.008365,YLR344W:0.010317,YLR367W:0.003094,YLR388W:0.021736,YML063W:0.006051,YMR121C:0.017411,YMR131C:0.026306,YNL119W:0.014916,YNL162W:0.016264,YNL302C:0.004123,YNR050C:0.058206,YOL121C:0.009887,YOL127W:0.013974,YOL040C:0.007057,YOR224C:0.013626,YOR254C:0.017923,YOR310C:0.006634,YOR312C:0.00351,YPL079W:0.030247,YPL131W:0.022146,YPL142C:0.015716,YPL220W:0.009552,YPL244C:0.022966,YPR102C:0.008204,YPR137W:0.017679)1:0.002907,((YBR032W:0.016097,YBR181C:0.009522,YBR187W:0.018681,YDR012W:0.011279,YGL102C:0.009205,YGR027C:0.00369,YJL157C:0.024018,YJL190C:0.007303,YLR058c:0.073551,YLR264W:0.018569,YLR300W:0.020115,YLR342W:0.034792,YLR359W:0.022991,YLR372W:0.011058,YMR300C:0.0321,YMR305C:0.014402,YNL069C:0.028621,YOR133W:0.004537,YOR167C:0.014198,YOR182C:0.023853,YOR326W:0.024632,YPL080C:0.064427,YPL081W:0.012279,YPL090C:0.012152)1:0.006473,(YOR298W:0.233587,((YDR019C:0.040149,YKL096W:0.037806)1:0.064948,(YKL108W:0.033111,YPR113W:0.038607)1:0.063282)1:0.016535)1:0.229462)1:0.024472)1:0.008239)1:0.017711)1:0.082401);'
Ago0000003="MATDNFYRMMILLEEPHKQHSTDGRKIENASHDFVDELLLPIQVDDLEVLNTWFDKFDEEICIPNEGHIKYEISSDGLIVLILDKEISEVIGLVRDFVAANQLDEDSSSDAK"
fasta_example = """
>Ago0000001
MFPSSATLLSFYAATSYVAALYVFPGRRIYGHASRNDPKAIWYGMKAVGCGVLANLLIIPWLQSRLAS
DGFSFVDCFFRLGLVPGAYAHFRGLHWDTLAYATDILRALSILGSLYAADLLDSAAYYLLVPDTSPVVDLVDRLSCTTGLRNYVFGPITEELVYTSMVLQNYRLLQPTISRAMLLLATPMFFGVAHVHHARQLLATGHRPAQVALTSSFQILYTTLFGTFT
NYIYYHTAGNLWACILLHAVCNYLSFPSLSSDVFADYCAKVPPALRALWKMRLLHAWGYTYRLCLLCGLLAFLDGIRTFSSSAGDLFLDA
>Ago0000002
MKADYTARASKTRGGQKVGGVRRESAGQGMSMSEDEFQAAQVRQRRSKSCAGPLEGVQERVLRAHTRQAKEKRKSEVLIAAQSLDYELQNVKNLKRISIGSMDLLMDPEMEFRMNGAAVSPSASPRNSLTEESLEWFQLSAEQEQGGELPLHAESIDAHSSAGGSSDTARDELLTSASSVVPSEELSCSHPLSPPAAAKKSTLMSSRSKLGRQHTDTTHTKQATGEPFS
SNLLWVRADQHPNVKPENYLELVHDTLNNLRIGARHGRGDSPVQQSNTPVANGESSTASARSLVRKQSRLRKSFTEVEAIEESQFTDSIGSEIPVGKRMRVSSLKEITEELTRISNNAGLTDSDAITLARTLGIGSQSADEHATFSECVPSAEAEENEYASSILAKNGLAIPARSSLRRSKFTTYRIRSAGSDSSPPENKSTSSSSLAAAYERNSRSPKMQKAAFKGSH
PRLSGENTSLAPQSPNSINDIYDHYNTSDTDDGSPELQGSPVTHTSDASFTSSPNIASGEHCARNAHKISPISVSQLSATSSSSTSPGSSKSAESTKSWTFDQKSPLRSITLNSSTKGHKISAEKKKGWSWFGNSRRPSSESVLLPGTDSEGCPMDESQPIQSEEYPLKHPISPVSDETPRRGNHSRNRHQTSSPEELEIGWTETSLTTLDGDTEQDGKPQHPKTKEKL
EKKFMKIFKKRSGTGLSQDTPNQGEESSLKATSRIRRSRESKRQTDEPSASLTTSVSLNNHNNGRKSVSISRPTWQRTESSYNGDKGKGSITSLQPAVSVTSSRDSHEQTRQDPQPQSLVTKMDGSSSNGVTVSSQRAGFSKKGRSKTSHSRSKLSTSHDIAPVDNRPSDVDQKSTEANNTLSSRAEDSHPSLDPGKSALGPGEIAHSLPPRKLRFDDVLRPEKPNSPM
KFTPSAFGFPLPPLTVSTVIMFDHRLPIYVERAIYRLSHLKLSDPKRELRQQVLLSNFMYSYLNLVNHSLYLQQIEEDKNQGIQFESTDNMASSSGVVPEKW
> Ago0000003"""+"\t"+"""Comment1"""+"\t"+"""Comment2
MATDNFYR MMILLEEPHK QHSTDGRKIENASHDFVDELLLPIQVDDLEVLNTWFDKFDEEICIPNEGHIKYEISSDGLIVLILDKEISEVIGLVRDFVAANQLDEDSSSDAK
> Ago0000004
MVSKTLPLYSKATLQKHTDRTSCWVSVGNRKIYDVSQFLDEHPGGDQYILDYAGKDITAVLKDKLIHEHTEAAYEILDESYLVGYLATEEEEIKLLTNEKHVMEVTPENLDTTTFVKELPAEEVLSVATDFGTDYTKHHFLDLNKPLLMQVLRGNFTRDFYIDQIHRPRHYGKGSAPLFGNFLEPLSKTVWWVVPMVWYPVVLYYLTRALQNMPAHLALTCFAAGVFVW
TLIEYSLHRFLFHFDDNMPESNIAFTVHFLLHGVHHYLPMDKYRLVMPPALFVVLCAPFYRLVFSIFPEYCACGCFAGGLFGYVCYDVTHYFLHHHKLPPFMRKLKKYHLEHHYKNYELGFGVTSWYWDKVFGTYLASNSPVSRPKCE
>Ago0000005
MYIKKVIIRGFKTYKNKTEIDNFSPHHNVVVGFNGSGKSNFFAAIRFVLSDDYTNLKREERRSLIYQGTSSVMSGYVEIVFHGAENRTLLGAQDGGVIHIRRTVGLKKDEYMINNKNASRSDVQRLLESAGFSTSNPYNIVPQGRIVSLTNAQNRERLQLLEEVIGAKSFERKLKESLQKMETTEKNREKIRIELEEVEAKLNELDEERKELEKYNSLDRKRKMCQFAL
YDRELNEVTSMVEKLDGEYTNTLVLSEQYIQELEKRESLIETLTKSLNQLGSELKMKESTDLQQAKDSELELAKHLADLNVKYEELISQNNALKEQSASNSESLLAIRSQIAVKEQQLARLSPRFEQLTIEEAAMKAEFKALQQRQRDLLAKRGKYSQFRNKAERDAWIDQELSILKEELQCSSIALTSISEERDSLRIKLTTLDDQIMELNDSAHGPGINAELEDVQQ
ELTVLKKAHLFKIDERKQLWRSEQKIQSVLESLVDDVKRAEGTLSETMDRSLATGLKNVSEIAQRLNLPEGSVFGPLGELIKISEKYKACAEVVGGTSLFHVVVDTENTAALLMQELYNSKGGRVTFIPLNRVHVDSNIVYPSNDEHHCTPLIKKIKYDPKFERAIKHVFGKTIVVKDLNQGTKLAKQFRLNAITLDGDKADSRGVLTGGFHDHHKQKRLDSMRDLKSL
KKEQQGNKSQLEEVKEKLHSIDQEIDELNDKIKKSMSRREMILTQVEAVNIKLEKAKRERFLLEETMVQLISKEEKAKINQKLLQDKLDMYTEDLSRDFDTELTLTEREELDEIAKKLPDLENLLNTTTDALSSVVVKIDSLKAELDSKLKPQAKELEDQPNEIMSTTAIQNLQEHIDAVEDERKTLLERKSTVDNEVQKISEIIDTLKSRQEEEEKSLEKANSQQRAL
LKKLDNYQKEAEKSMLRKMTLSTRRDELQQKIRDIGLLPDDSADKYHNMSSSELLKELSSINDKISKMTNVNKRALENFKKFDDKQKDVMKRAKELDESKESIEKLIDKLKKQKVEAVENTFKKVSENFTQLFEKMVPRGTGKLVIHRRENEPSKPSKRQQKKRKRQETEDVHFNDDQDENSSQDSIYSGVSIEVSFNSKKDEQVHVEQLSGGQKTVCAIALILAIQMV
DPAPFYLFDEIDAALDKQYRTAVAATVKQLSSQAQFICTTFRGDMIAVADRFYRVNFENKISTVVEVTKAEALNFVTGREKNENVI
> Ago0000006
MYKLQVVLVPPSIETELPVVGLPAGSLDNSGFAQGHAQPISTSSIAGGRGEFSSGIGNTSANAVYLSGLVGAHIRRARGRKFLHFTKPTNSLYELADEIVEKCAKMYPGLAEEPEIVTLQDVNECDLDPDFVVKDVFNMDNTVRVLLRNDLDEAAGDRTIYMKKRKLNTGAAGVPAAGGSVQAAVLNVAKKRASIKTSALRVSTPLANQIYPPPTKKQVNSDFEDDDVA
DKSILPPPPPQSPPIRISSGMDQKRINMNDNAVSKSETVDPNKSRQQRLPSGTPMRPVSMVETPNRVSLTGPTVLSESTVSQKSTATPIITNIRITSGMLRIPEPRLSEVEKELKEGPASPAVDLPARPSRIPMKKPYNPSMQQDEDLSSSSSSTEDNVPAVPYENELERSGPTMATRQSSSTIADDQGSPTKKSRFEKNNIGLVELPSPRKSSLEKKVSKLNKGLASD
KGHEDSTGGITRKDHFSDEESEASQNGSVVVNRPETQREKSFQKSELLKIFNSKRFDLPPRFKNSASEDEPTSSNQSRKKKPYVTVLNKDIDNSSPDPRNIIPRRTQRHAAQKAAQSISSGTSRSNVFSGEEKNKYSEENQGDNIASDDNEGVYVHESNALKKLNVHPLKESVVQDTLTGAQDINNPVSSRTVHPSISEHAVTAAASGTLSSNPEYRVAPIVTPTLMSS
AVPGKPEAILSKQGDPPASTALKPQLAPARKVESTQKKQAGKKSDTNQPSRTNSKKTGLPADTAVPSSQKTVRARAAQIDAQIKQTATSSQSPVAESQSSVLNSEEAVADKSEVDNNSSTQDKSLQQKTSKRKTPVKRTANADKKAVTLKRSSNSKGKEKDTEKGKERIKEKEKEKEKEKEKEKEKVYQTPEFVESSDDERADAKTPLEKHSSDRPKSGSPSKHENGQE
KQDSFSGIILKKTAIEKDKVVANAPHKVNEKPMTADAGSTNLSPSGKVSKLDELRSKFTKGRFPQGSSQKQIQQQKNTPKTSSKSIVPTVSDKFKPMDSTSGASSDDSADDDDDDSMDSSTEDEGISMKKPRRGIVQPPKGSVSAPVKHVPQSLSSELEGVPQSTQIPNEATNTAPLTKLLDHISPPSTAKTITSRGVTESKGTSNRSLSSLSDLASRGVPDVREKGVN
YKKTAPNVVNNSSSDESEQETNDGSDSSDSDNSDSDSSDSSDDGNNFISAKSASKALRKNKASSGFASLIRDSQKK
>Ago0000007
MGSLQAREMEELYVYSGENMPRVRLCLLRRYSCVEEVEAYVGRVQDRYTLRLGTVETITGNLKIGCDTHADCEACPFYILEYNEVTTEYSLWKAADADWRLDSIVATMYTGAGGPARERGGLPRELQGLREGLDMEYVWDCLRRLNLPLEQIDWAEFRELLESMLAAKRVADDDCVTLRGVVALAALQATVQTSKRAVRSQLRAYDRRVRAASTPASTRTSSPESLLPA
DSRESSVSSVHYTYGLPATQLDANFKTYFRSMAENFELFEEPALALRGRVAKPRKKAAGRHGHRPVQA
>Ago0000008
MQISAVALSGAALLACASAHQHDRKKPHLVVVYGDVYVSGTDTFTKYYSKMTDKLPASGSDGWSYSWSTATSWTSDSVSTEPSAEPTSTEPTNLPEVTSSPATPVQPTSAPEETFEEPTESTSAEPTSSPEPVKSAEPTSSPEPVKSVEPTSSPEPVKSVEPVKSAEPVKSPEPVKSPEPVKSPEPVKSPEPVKSAEPTSSPEPTGSPQRSRPAGGQNGASFEEEILRA
HNSRRQLHKDTKPLTWSEELAKFARDFANQYDCSGRLVHSDSPYGENLAVGYPTPEKAVKAWYDEISDYSYSHPSFSFSTGHFSQLVWKDTKHLGCAVKKCGGSVGDYLICSYDPAGNFLRRFGENVAPIA
>Ago0000009
MRACLLIPLLLVAATARTVTVSVTATRTVTVISAAAVTTLRTTVFTTAYRTQTTPLTETPLSRPTAVNNTFASAVLDLHNDYRRRHHAVPLRWNSTLYTHAQHYANRILCNGSLVHSGLPHGENLALGYSPAAAVTAWYDEIAEYDFSTPGFSHATGHFTQLVWRSTTSVGCAYVMCGPCYGLYIICQYDPPGNVADQYVANVLP
>Ago0000010
MESQAAVEEPQHSVVIETPPTTAESSETPVADTATGAEPEGAGGAAVVAPKRMPTRADFPPLSSVIFETQKVQWGPNMKKPESQSASPSPSPGPVGSGAKPMRSKTMQEAFSLDLQTQVTISKAEFSKFVVSVKQSHSVSIESTLSKLSRTFLITGSPTNVYNAKRELVKKLTRPVTVVIQVPSKTVSSIIGPGGRMIREITNAAGGIKIDIAKTAEADAYDADLDDQL
INISLHGDVASVNFAKDKILSIVKEETKNATISVAVENKQLIPFISLADVEISEDVTVKAFPNGSEKIVLMGPRDEAKEAKVNVQNYLNTLASKVSEKKISIPRKFQPLIDAEDVREKYKVSVIFPTALGDDTVSFYGLSANLDDAIAYARQSSKQYIVESLEVSKAHGKNVAHAKNLMFYFAKYDILKDIKESFKEVKLVLPTPEELPGLDNVSINIISKADIAEQTK
TVRKQIINIVNRLTPSHVLAVDDLDYELFHKDIKQALSKAEIPFVQLGDHYEGDNTVLLFAKVDEEDFQPSPEEVKEHLEKVAAVLDEVRTKQSKLFTKIVNFDAEFQVLHFSDDSVTWNLVLENITSAGGHAQIKLHTPSEDEITIRGDEKAVKAAVKAFESIAENPSKKSKLTVSVPANTVSRLIGPKGTNLAQIRQKFDVQIDVPSESNDTNTEITLTGLEYNLQH
AKTHIASEAKKWADITTKELIVPTKYHGSLIGSQGTYRIRLENKYSVRIQFPKEGEVVTIKGPSRGVNKAHAELKALLDFEIENGHKSVINVPVEHVPRVIGKNGDVINGIRAELGVELKLLQNTKTAKEQNLDTVQLEITGSRQAIKEASKAVDAIIAEASDFTTKQLEIDAKYHKLIVGPGGSTLKDFISKAGGDDIRNKTVDVPNAESTNKVITISGPKTFVEKMS
KALNQIVQDIKASVAKELNIPADRQGALIGPGGSVRRQLESQFNVRIEVPDKGKEGKVTIHGRPEAVEKCEKEIFSTIIRDSYDQEIMVPAVYHAFVSERGQLINKLRMTYFINVKHGNSSKKANKLSRSEQPIPIERVRGSEGEGTKLTIEEVSAPEASANDNIPWRLTYEHVDLSDILGEEGKHAMTKEQALEAAADQIKERIELAPKANCIGYLWCENVKKFNKVV
GPGGSNIKQIRETTNTLINVPKKSDKVSDIIYVRGTKESVEKACKMICDALNK
"""
fasta_example_output = """>Ago0000001
MFPSSATLLSFYAATSYVAALYVFPGRRIYGHASRNDPKAIWYGMKAVGCGVLANLLIIPWLQSRLASDGFSFVDCFFRL
GLVPGAYAHFRGLHWDTLAYATDILRALSILGSLYAADLLDSAAYYLLVPDTSPVVDLVDRLSCTTGLRNYVFGPITEEL
VYTSMVLQNYRLLQPTISRAMLLLATPMFFGVAHVHHARQLLATGHRPAQVALTSSFQILYTTLFGTFTNYIYYHTAGNL
WACILLHAVCNYLSFPSLSSDVFADYCAKVPPALRALWKMRLLHAWGYTYRLCLLCGLLAFLDGIRTFSSSAGDLFLDA
>Ago0000002
MKADYTARASKTRGGQKVGGVRRESAGQGMSMSEDEFQAAQVRQRRSKSCAGPLEGVQERVLRAHTRQAKEKRKSEVLIA
AQSLDYELQNVKNLKRISIGSMDLLMDPEMEFRMNGAAVSPSASPRNSLTEESLEWFQLSAEQEQGGELPLHAESIDAHS
SAGGSSDTARDELLTSASSVVPSEELSCSHPLSPPAAAKKSTLMSSRSKLGRQHTDTTHTKQATGEPFSSNLLWVRADQH
PNVKPENYLELVHDTLNNLRIGARHGRGDSPVQQSNTPVANGESSTASARSLVRKQSRLRKSFTEVEAIEESQFTDSIGS
EIPVGKRMRVSSLKEITEELTRISNNAGLTDSDAITLARTLGIGSQSADEHATFSECVPSAEAEENEYASSILAKNGLAI
PARSSLRRSKFTTYRIRSAGSDSSPPENKSTSSSSLAAAYERNSRSPKMQKAAFKGSHPRLSGENTSLAPQSPNSINDIY
DHYNTSDTDDGSPELQGSPVTHTSDASFTSSPNIASGEHCARNAHKISPISVSQLSATSSSSTSPGSSKSAESTKSWTFD
QKSPLRSITLNSSTKGHKISAEKKKGWSWFGNSRRPSSESVLLPGTDSEGCPMDESQPIQSEEYPLKHPISPVSDETPRR
GNHSRNRHQTSSPEELEIGWTETSLTTLDGDTEQDGKPQHPKTKEKLEKKFMKIFKKRSGTGLSQDTPNQGEESSLKATS
RIRRSRESKRQTDEPSASLTTSVSLNNHNNGRKSVSISRPTWQRTESSYNGDKGKGSITSLQPAVSVTSSRDSHEQTRQD
PQPQSLVTKMDGSSSNGVTVSSQRAGFSKKGRSKTSHSRSKLSTSHDIAPVDNRPSDVDQKSTEANNTLSSRAEDSHPSL
DPGKSALGPGEIAHSLPPRKLRFDDVLRPEKPNSPMKFTPSAFGFPLPPLTVSTVIMFDHRLPIYVERAIYRLSHLKLSD
PKRELRQQVLLSNFMYSYLNLVNHSLYLQQIEEDKNQGIQFESTDNMASSSGVVPEKW
>Ago0000003"""+"\t"+"""Comment1"""+"\t"+"""Comment2
MATDNFYRMMILLEEPHKQHSTDGRKIENASHDFVDELLLPIQVDDLEVLNTWFDKFDEEICIPNEGHIKYEISSDGLIV
LILDKEISEVIGLVRDFVAANQLDEDSSSDAK
>Ago0000004
MVSKTLPLYSKATLQKHTDRTSCWVSVGNRKIYDVSQFLDEHPGGDQYILDYAGKDITAVLKDKLIHEHTEAAYEILDES
YLVGYLATEEEEIKLLTNEKHVMEVTPENLDTTTFVKELPAEEVLSVATDFGTDYTKHHFLDLNKPLLMQVLRGNFTRDF
YIDQIHRPRHYGKGSAPLFGNFLEPLSKTVWWVVPMVWYPVVLYYLTRALQNMPAHLALTCFAAGVFVWTLIEYSLHRFL
FHFDDNMPESNIAFTVHFLLHGVHHYLPMDKYRLVMPPALFVVLCAPFYRLVFSIFPEYCACGCFAGGLFGYVCYDVTHY
FLHHHKLPPFMRKLKKYHLEHHYKNYELGFGVTSWYWDKVFGTYLASNSPVSRPKCE
>Ago0000005
MYIKKVIIRGFKTYKNKTEIDNFSPHHNVVVGFNGSGKSNFFAAIRFVLSDDYTNLKREERRSLIYQGTSSVMSGYVEIV
FHGAENRTLLGAQDGGVIHIRRTVGLKKDEYMINNKNASRSDVQRLLESAGFSTSNPYNIVPQGRIVSLTNAQNRERLQL
LEEVIGAKSFERKLKESLQKMETTEKNREKIRIELEEVEAKLNELDEERKELEKYNSLDRKRKMCQFALYDRELNEVTSM
VEKLDGEYTNTLVLSEQYIQELEKRESLIETLTKSLNQLGSELKMKESTDLQQAKDSELELAKHLADLNVKYEELISQNN
ALKEQSASNSESLLAIRSQIAVKEQQLARLSPRFEQLTIEEAAMKAEFKALQQRQRDLLAKRGKYSQFRNKAERDAWIDQ
ELSILKEELQCSSIALTSISEERDSLRIKLTTLDDQIMELNDSAHGPGINAELEDVQQELTVLKKAHLFKIDERKQLWRS
EQKIQSVLESLVDDVKRAEGTLSETMDRSLATGLKNVSEIAQRLNLPEGSVFGPLGELIKISEKYKACAEVVGGTSLFHV
VVDTENTAALLMQELYNSKGGRVTFIPLNRVHVDSNIVYPSNDEHHCTPLIKKIKYDPKFERAIKHVFGKTIVVKDLNQG
TKLAKQFRLNAITLDGDKADSRGVLTGGFHDHHKQKRLDSMRDLKSLKKEQQGNKSQLEEVKEKLHSIDQEIDELNDKIK
KSMSRREMILTQVEAVNIKLEKAKRERFLLEETMVQLISKEEKAKINQKLLQDKLDMYTEDLSRDFDTELTLTEREELDE
IAKKLPDLENLLNTTTDALSSVVVKIDSLKAELDSKLKPQAKELEDQPNEIMSTTAIQNLQEHIDAVEDERKTLLERKST
VDNEVQKISEIIDTLKSRQEEEEKSLEKANSQQRALLKKLDNYQKEAEKSMLRKMTLSTRRDELQQKIRDIGLLPDDSAD
KYHNMSSSELLKELSSINDKISKMTNVNKRALENFKKFDDKQKDVMKRAKELDESKESIEKLIDKLKKQKVEAVENTFKK
VSENFTQLFEKMVPRGTGKLVIHRRENEPSKPSKRQQKKRKRQETEDVHFNDDQDENSSQDSIYSGVSIEVSFNSKKDEQ
VHVEQLSGGQKTVCAIALILAIQMVDPAPFYLFDEIDAALDKQYRTAVAATVKQLSSQAQFICTTFRGDMIAVADRFYRV
NFENKISTVVEVTKAEALNFVTGREKNENVI
>Ago0000006
MYKLQVVLVPPSIETELPVVGLPAGSLDNSGFAQGHAQPISTSSIAGGRGEFSSGIGNTSANAVYLSGLVGAHIRRARGR
KFLHFTKPTNSLYELADEIVEKCAKMYPGLAEEPEIVTLQDVNECDLDPDFVVKDVFNMDNTVRVLLRNDLDEAAGDRTI
YMKKRKLNTGAAGVPAAGGSVQAAVLNVAKKRASIKTSALRVSTPLANQIYPPPTKKQVNSDFEDDDVADKSILPPPPPQ
SPPIRISSGMDQKRINMNDNAVSKSETVDPNKSRQQRLPSGTPMRPVSMVETPNRVSLTGPTVLSESTVSQKSTATPIIT
NIRITSGMLRIPEPRLSEVEKELKEGPASPAVDLPARPSRIPMKKPYNPSMQQDEDLSSSSSSTEDNVPAVPYENELERS
GPTMATRQSSSTIADDQGSPTKKSRFEKNNIGLVELPSPRKSSLEKKVSKLNKGLASDKGHEDSTGGITRKDHFSDEESE
ASQNGSVVVNRPETQREKSFQKSELLKIFNSKRFDLPPRFKNSASEDEPTSSNQSRKKKPYVTVLNKDIDNSSPDPRNII
PRRTQRHAAQKAAQSISSGTSRSNVFSGEEKNKYSEENQGDNIASDDNEGVYVHESNALKKLNVHPLKESVVQDTLTGAQ
DINNPVSSRTVHPSISEHAVTAAASGTLSSNPEYRVAPIVTPTLMSSAVPGKPEAILSKQGDPPASTALKPQLAPARKVE
STQKKQAGKKSDTNQPSRTNSKKTGLPADTAVPSSQKTVRARAAQIDAQIKQTATSSQSPVAESQSSVLNSEEAVADKSE
VDNNSSTQDKSLQQKTSKRKTPVKRTANADKKAVTLKRSSNSKGKEKDTEKGKERIKEKEKEKEKEKEKEKEKVYQTPEF
VESSDDERADAKTPLEKHSSDRPKSGSPSKHENGQEKQDSFSGIILKKTAIEKDKVVANAPHKVNEKPMTADAGSTNLSP
SGKVSKLDELRSKFTKGRFPQGSSQKQIQQQKNTPKTSSKSIVPTVSDKFKPMDSTSGASSDDSADDDDDDSMDSSTEDE
GISMKKPRRGIVQPPKGSVSAPVKHVPQSLSSELEGVPQSTQIPNEATNTAPLTKLLDHISPPSTAKTITSRGVTESKGT
SNRSLSSLSDLASRGVPDVREKGVNYKKTAPNVVNNSSSDESEQETNDGSDSSDSDNSDSDSSDSSDDGNNFISAKSASK
ALRKNKASSGFASLIRDSQKK
>Ago0000007
MGSLQAREMEELYVYSGENMPRVRLCLLRRYSCVEEVEAYVGRVQDRYTLRLGTVETITGNLKIGCDTHADCEACPFYIL
EYNEVTTEYSLWKAADADWRLDSIVATMYTGAGGPARERGGLPRELQGLREGLDMEYVWDCLRRLNLPLEQIDWAEFREL
LESMLAAKRVADDDCVTLRGVVALAALQATVQTSKRAVRSQLRAYDRRVRAASTPASTRTSSPESLLPADSRESSVSSVH
YTYGLPATQLDANFKTYFRSMAENFELFEEPALALRGRVAKPRKKAAGRHGHRPVQA
>Ago0000008
MQISAVALSGAALLACASAHQHDRKKPHLVVVYGDVYVSGTDTFTKYYSKMTDKLPASGSDGWSYSWSTATSWTSDSVST
EPSAEPTSTEPTNLPEVTSSPATPVQPTSAPEETFEEPTESTSAEPTSSPEPVKSAEPTSSPEPVKSVEPTSSPEPVKSV
EPVKSAEPVKSPEPVKSPEPVKSPEPVKSPEPVKSAEPTSSPEPTGSPQRSRPAGGQNGASFEEEILRAHNSRRQLHKDT
KPLTWSEELAKFARDFANQYDCSGRLVHSDSPYGENLAVGYPTPEKAVKAWYDEISDYSYSHPSFSFSTGHFSQLVWKDT
KHLGCAVKKCGGSVGDYLICSYDPAGNFLRRFGENVAPIA
>Ago0000009
MRACLLIPLLLVAATARTVTVSVTATRTVTVISAAAVTTLRTTVFTTAYRTQTTPLTETPLSRPTAVNNTFASAVLDLHN
DYRRRHHAVPLRWNSTLYTHAQHYANRILCNGSLVHSGLPHGENLALGYSPAAAVTAWYDEIAEYDFSTPGFSHATGHFT
QLVWRSTTSVGCAYVMCGPCYGLYIICQYDPPGNVADQYVANVLP
>Ago0000010
MESQAAVEEPQHSVVIETPPTTAESSETPVADTATGAEPEGAGGAAVVAPKRMPTRADFPPLSSVIFETQKVQWGPNMKK
PESQSASPSPSPGPVGSGAKPMRSKTMQEAFSLDLQTQVTISKAEFSKFVVSVKQSHSVSIESTLSKLSRTFLITGSPTN
VYNAKRELVKKLTRPVTVVIQVPSKTVSSIIGPGGRMIREITNAAGGIKIDIAKTAEADAYDADLDDQLINISLHGDVAS
VNFAKDKILSIVKEETKNATISVAVENKQLIPFISLADVEISEDVTVKAFPNGSEKIVLMGPRDEAKEAKVNVQNYLNTL
ASKVSEKKISIPRKFQPLIDAEDVREKYKVSVIFPTALGDDTVSFYGLSANLDDAIAYARQSSKQYIVESLEVSKAHGKN
VAHAKNLMFYFAKYDILKDIKESFKEVKLVLPTPEELPGLDNVSINIISKADIAEQTKTVRKQIINIVNRLTPSHVLAVD
DLDYELFHKDIKQALSKAEIPFVQLGDHYEGDNTVLLFAKVDEEDFQPSPEEVKEHLEKVAAVLDEVRTKQSKLFTKIVN
FDAEFQVLHFSDDSVTWNLVLENITSAGGHAQIKLHTPSEDEITIRGDEKAVKAAVKAFESIAENPSKKSKLTVSVPANT
VSRLIGPKGTNLAQIRQKFDVQIDVPSESNDTNTEITLTGLEYNLQHAKTHIASEAKKWADITTKELIVPTKYHGSLIGS
QGTYRIRLENKYSVRIQFPKEGEVVTIKGPSRGVNKAHAELKALLDFEIENGHKSVINVPVEHVPRVIGKNGDVINGIRA
ELGVELKLLQNTKTAKEQNLDTVQLEITGSRQAIKEASKAVDAIIAEASDFTTKQLEIDAKYHKLIVGPGGSTLKDFISK
AGGDDIRNKTVDVPNAESTNKVITISGPKTFVEKMSKALNQIVQDIKASVAKELNIPADRQGALIGPGGSVRRQLESQFN
VRIEVPDKGKEGKVTIHGRPEAVEKCEKEIFSTIIRDSYDQEIMVPAVYHAFVSERGQLINKLRMTYFINVKHGNSSKKA
NKLSRSEQPIPIERVRGSEGEGTKLTIEEVSAPEASANDNIPWRLTYEHVDLSDILGEEGKHAMTKEQALEAAADQIKER
IELAPKANCIGYLWCENVKKFNKVVGPGGSNIKQIRETTNTLINVPKKSDKVSDIIYVRGTKESVEKACKMICDALNK
"""
CYS1_DICDI="-----MKVILLFVLAVFTVFVSS---------------RGIPPEEQ------------SQFLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRG-AVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIP-KNETVMAGYIVSTGPLAIAADAVE-WQFYIGGVF-DIPCN--PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII--"
phylip_interlived = """ 3 384
CYS1_DICDI -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ---- --------SQ
ALEU_HORVU MAHARVLLLA LAVLATAAVA VASSSSFADS NPIRPVTDRA ASTLESAVLG ALGRTRHALR
CATH_HUMAN ------MWAT LPLLCAGAWL LGV------- -PVCGAAELS VNSLEK---- --------FH
FLEFQDKFNK KY-SHEEYLE RFEIFKSNLG KIEELNLIAI NHKADTKFGV NKFADLSSDE
FARFAVRYGK SYESAAEVRR RFRIFSESLE EVRSTN---- RKGLPYRLGI NRFSDMSWEE
FKSWMSKHRK TY-STEEYHH RLQTFASNWR KINAHN---- NGNHTFKMAL NQFSDMSFAE
FKNYYLNNKE AIFTDDLPVA DYLDDEFINS IPTAFDWRTR G-AVTPVKNQ GQCGSCWSFS
FQATRL-GAA QTCSATLAGN HLMRDA--AA LPETKDWRED G-IVSPVKNQ AHCGSCWTFS
IKHKYLWSEP QNCSAT--KS NYLRGT--GP YPPSVDWRKK GNFVSPVKNQ GACGSCWTFS
TTGNVEGQHF ISQNKLVSLS EQNLVDCDHE CMEYEGEEAC DEGCNGGLQP NAYNYIIKNG
TTGALEAAYT QATGKNISLS EQQLVDCAGG FNNF------ --GCNGGLPS QAFEYIKYNG
TTGALESAIA IATGKMLSLA EQQLVDCAQD FNNY------ --GCQGGLPS QAFEYILYNK
GIQTESSYPY TAETGTQCNF NSANIGAKIS NFTMIP-KNE TVMAGYIVST GPLAIAADAV
GIDTEESYPY KGVNGV-CHY KAENAAVQVL DSVNITLNAE DELKNAVGLV RPVSVAFQVI
GIMGEDTYPY QGKDGY-CKF QPGKAIGFVK DVANITIYDE EAMVEAVALY NPVSFAFEVT
E-WQFYIGGV F-DIPCN--P NSLDHGILIV GYSAKNTIFR KNMPYWIVKN SWGADWGEQG
DGFRQYKSGV YTSDHCGTTP DDVNHAVLAV GYGVENGV-- ---PYWLIKN SWGADWGDNG
QDFMMYRTGI YSSTSCHKTP DKVNHAVLAV GYGEKNGI-- ---PYWIVKN SWGPQWGMNG
YIYLRRGKNT CGVSNFVSTS II--
YFKMEMGKNM CAIATCASYP VVAA
YFLIERGKNM CGLAACASYP IPLV
"""
phylip_sequencial = """ 3 384
CYS1_DICDI -----MKVILLFVLAVFTVFVSS---------------RGIPPEEQ-
-----------SQFLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTK
FGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRG-AVTPV
KNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGG
LQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIP-KNETVMAGYI
VSTGPLAIAADAVE-WQFYIGGVF-DIPCN--PNSLDHGILIVGYSAKNTIFRKNMPYWI
VKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII--
ALEU_HORVU MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESA
VLGALGRTRHALRFARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTN----RKGLPYR
LGINRFSDMSWEEFQATRL-GAAQTCSATLAGNHLMRDA--AALPETKDWREDG-IVSPV
KNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNF--------GCNGG
LPSQAFEYIKYNGGIDTEESYPYKGVNGV-CHYKAENAAVQVLDSVNITLNAEDELKNAV
GLVRPVSVAFQVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGV-----PYWL
IKNSWGADWGDNGYFKMEMGKNMCAIATCASYPVVAA
CATH_HUMAN ------MWATLPLLCAGAWLLGV--------PVCGAAELSVNSLEK-
-----------FHFKSWMSKHRKTY-STEEYHHRLQTFASNWRKINAHN----NGNHTFK
MALNQFSDMSFAEIKHKYLWSEPQNCSAT--KSNYLRGT--GPYPPSVDWRKKGNFVSPV
KNQGACGSCWTFSTTGALESAIAIATGKMLSLAEQQLVDCAQDFNNY--------GCQGG
LPSQAFEYILYNKGIMGEDTYPYQGKDGY-CKFQPGKAIGFVKDVANITIYDEEAMVEAV
ALYNPVSFAFEVTQDFMMYRTGIYSSTSCHKTPDKVNHAVLAVGYGEKNGI-----PYWI
VKNSWGPQWGMNGYFLIERGKNMCGLAACASYPIPLV
"""
expression = '#Names\tcol1\tcol2\tcol3\tcol4\tcol5\tcol6\tcol7\nA\t-1.23\t-0.81\t1.79\t0.78\t-0.42\t-0.69\t0.58\nB\t-1.76\t-0.94\t1.16\t0.36\t0.41\t-0.35\t1.12\nC\t-2.19\t0.13\t0.65\t-0.51\t0.52\t1.04\t0.36\nD\t-1.22\t-0.98\t0.79\t-0.76\t-0.29\t1.54\t0.93\nE\t-1.47\t-0.83\t0.85\t0.07\t-0.81\t1.53\t0.65\nF\t-1.04\t-1.11\t0.87\t-0.14\t-0.80\t1.74\t0.48\nG\t-1.57\t-1.17\t1.29\t0.23\t-0.20\t1.17\t0.26\nH\t-1.53\t-1.25\t0.59\t-0.30\t0.32\t1.41\t0.77\n'
|
