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Error when parsing tree with Fbranch #22
Comments
Hi Mike Kind regards |
Hi Milan,
Thanks for the response. I couldn't spot any errors, but I did have issues
with another dataset until I got rid of unnecessary brackets and then it
worked, so perhaps it is something similar to this.
I have attached the combined_tree.txt and tree.nwk files.
Many thanks,
Mike
On Thu, 23 Jul 2020 at 17:17, Milan Malinsky ***@***.***> wrote:
Hi Mike
My best guess would be a spelling error in your tree file. If you can't
figure it out, feel free to email me with your combined_tree.txt and the
tree.nwk files, I can try to investigate.
Kind regards
Milan
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.
P1 P2 P3 Dstatistic p-value f_G
AA-005 AA-009 AA-006 0.0468455 1.49691e-12 0.102669
AA-012 AA-005 AA-006 0.0149881 0.0800367 0.0374971
AA-006 AA-015 AA-005 0.019906 0.00118937 0.0675076
AA-006 AA-019 AA-005 0.0135085 0.0236758 0.0435013
AA-005 AB-11A AA-006 0.0353714 6.5595e-09 0.0662756
AA-005 AA-006 AG-018 0.0368183 3.98615e-06 0.0392163
AA-005 AA-006 AG-021 0.0424143 1.23812e-08 0.0557566
AA-005 AA-006 AG-024 0.0466992 6.65259e-10 0.0603276
AL-005 AA-005 AA-006 0.0431316 2.75206e-10 0.0746817
AL-009 AA-005 AA-006 0.0241848 0.00018271 0.0445046
AL-012 AA-005 AA-006 0.0669946 1.00281e-11 0.136393
AL-11B AA-005 AA-006 0.0506957 1.19443e-11 0.0921582
AN-005 AA-005 AA-006 0.0224954 0.00076791 0.0445604
AN-012 AA-005 AA-006 0.0304152 0.000869259 0.0754311
AN-11A AA-005 AA-006 0.0299459 4.12198e-05 0.065286
AA-006 AU-015 AA-005 0.00836856 0.116227 0.027258
AA-005 AY-11A AA-006 0.023625 0.000100665 0.0509617
AA-012 AA-005 AA-009 0.00836941 0.203575 0.0288418
AA-005 AA-009 AA-015 0.0247747 9.79364e-05 0.056788
AA-005 AA-009 AA-019 0.0415933 3.4707e-09 0.0936612
AA-005 AB-11A AA-009 0.021721 0.000405854 0.0532342
AA-005 AA-009 AG-018 0.0102481 0.0965598 0.010998
AA-005 AA-009 AG-021 0.0245523 0.000898289 0.0333271
AA-005 AA-009 AG-024 0.0195981 0.00734492 0.0256938
AL-005 AA-005 AA-009 0.0428893 2.77386e-10 0.0923457
AL-009 AA-005 AA-009 0.00453909 0.245834 0.0107281
AL-012 AA-005 AA-009 0.0423595 1.92103e-06 0.117695
AL-11B AA-005 AA-009 0.0383771 3.69323e-07 0.0927388
AN-005 AA-005 AA-009 0.0068375 0.166972 0.0176327
AN-012 AA-005 AA-009 0.00530299 0.298329 0.0198073
AN-11A AA-005 AA-009 0.00689551 0.197184 0.0202452
AA-005 AA-009 AU-015 0.0261653 6.17571e-05 0.0565042
AA-005 AY-11A AA-009 0.0112397 0.0378089 0.0309657
AA-012 AA-005 AA-015 0.0114553 0.131552 0.0309638
AA-012 AA-005 AA-019 0.00472052 0.32437 0.0146604
AA-005 AA-012 AB-11A 0.0149665 0.0344006 0.065883
AA-012 AA-005 AG-018 0.0218494 0.0224195 0.0240296
AA-012 AA-005 AG-021 0.00577335 0.291216 0.0103492
AA-012 AA-005 AG-024 0.00732958 0.286211 0.0117702
AL-005 AA-005 AA-012 0.0451408 2.12229e-06 0.0760672
AL-009 AA-005 AA-012 0.0374299 9.8155e-05 0.0652853
AL-012 AA-005 AA-012 0.0216015 0.030604 0.0388137
AL-11B AA-005 AA-012 0.0300127 0.00311626 0.0528382
AN-005 AA-005 AA-012 0.00133655 0.442199 0.00244031
AA-005 AN-012 AA-012 0.0233243 0.0114422 0.0490005
AA-005 AN-11A AA-012 0.0116136 0.123901 0.0214573
AA-005 AA-012 AU-015 0.00787839 0.221807 0.0238448
AA-005 AA-012 AY-11A 0.0261944 0.00254363 0.105018
AA-019 AA-015 AA-005 0.00719321 0.145379 0.0250326
AA-005 AB-11A AA-015 0.0301669 3.16955e-07 0.0631219
AA-005 AA-015 AG-018 0.0486449 1.47097e-08 0.051592
AA-005 AA-015 AG-021 0.0477647 2.64153e-10 0.0641342
AA-005 AA-015 AG-024 0.0524769 6.569e-10 0.0669473
AL-005 AA-005 AA-015 0.0475089 1.36557e-14 0.0851553
AL-009 AA-005 AA-015 0.0360516 1.47138e-08 0.0644852
AL-012 AA-005 AA-015 0.0540119 6.96737e-09 0.129286
AL-11B AA-005 AA-015 0.0527641 1.66622e-12 0.0972208
AN-005 AA-005 AA-015 0.0309157 2.61273e-06 0.0612131
AN-012 AA-005 AA-015 0.0263766 0.00481586 0.0696488
AN-11A AA-005 AA-015 0.0217225 0.00186733 0.049033
AU-015 AA-015 AA-005 0.00910279 0.0636963 0.0306638
AA-005 AY-11A AA-015 0.0126924 0.0238988 0.0271075
AA-005 AB-11A AA-019 0.0349646 3.42298e-09 0.0740618
AA-005 AA-019 AG-018 0.0514907 3.8895e-10 0.0533056
AA-005 AA-019 AG-021 0.0595182 4.54081e-14 0.0754757
AA-005 AA-019 AG-024 0.0492429 4.58709e-09 0.0624832
AL-005 AA-005 AA-019 0.0521748 2.02061e-14 0.0951167
AL-009 AA-005 AA-019 0.0249675 8.62109e-05 0.0468451
AL-012 AA-005 AA-019 0.0671418 5.19584e-13 0.159433
AL-11B AA-005 AA-019 0.0554555 8.49321e-14 0.111337
AN-005 AA-005 AA-019 0.0228072 0.000836856 0.0491566
AN-012 AA-005 AA-019 0.0347773 0.000193 0.104613
AN-11A AA-005 AA-019 0.0277831 0.000327084 0.0646915
AU-015 AA-019 AA-005 0.00194189 0.380386 0.00625479
AA-005 AY-11A AA-019 0.0183857 0.00272876 0.0398517
AA-005 AB-11A AG-018 0.0113182 0.0661613 0.0116927
AA-005 AB-11A AG-021 0.02242 0.000842982 0.0277628
AA-005 AB-11A AG-024 0.024023 0.00028821 0.0297834
AL-005 AA-005 AB-11A 0.0377125 4.11213e-10 0.100416
AL-009 AA-005 AB-11A 0.0336517 6.45357e-08 0.0913126
AL-012 AA-005 AB-11A 0.0308334 0.00021232 0.117709
AL-11B AA-005 AB-11A 0.0206703 0.00137192 0.0637906
AN-005 AA-005 AB-11A 0.00917324 0.0920388 0.0301151
AN-012 AA-005 AB-11A 0.00478075 0.305343 0.0217181
AA-005 AN-11A AB-11A 0.00522671 0.236664 0.0196903
AA-005 AB-11A AU-015 0.0329006 1.19052e-08 0.0652148
AY-11A AB-11A AA-005 0.0128701 0.014562 0.0439126
AG-018 AG-021 AA-005 0.00479303 0.27412 0.0106463
AG-018 AG-024 AA-005 0.0224512 0.00884197 0.0652512
AL-005 AA-005 AG-018 0.0347754 1.09655e-05 0.0337696
AL-009 AA-005 AG-018 0.0302027 7.21986e-05 0.0298452
AL-012 AA-005 AG-018 0.0502735 4.43879e-06 0.0530217
AL-11B AA-005 AG-018 0.0370589 1.50716e-05 0.0369344
AN-005 AA-005 AG-018 0.0233658 0.00184561 0.0237507
AN-012 AA-005 AG-018 0.0326419 0.00491073 0.0372251
AN-11A AA-005 AG-018 0.0315828 0.000191078 0.0324871
AA-005 AU-015 AG-018 0.0417591 3.8215e-07 0.0439833
AA-005 AY-11A AG-018 0.00432402 0.288393 0.00456723
AG-021 AG-024 AA-005 0.0124397 0.0830825 0.0362322
AL-005 AA-005 AG-021 0.0328566 6.67745e-06 0.0391146
AL-009 AA-005 AG-021 0.0241987 0.000606205 0.0292354
AL-012 AA-005 AG-021 0.0370725 0.000101074 0.0585847
AL-11B AA-005 AG-021 0.0258468 0.000790923 0.032178
AN-005 AA-005 AG-021 0.0174032 0.01131 0.0224976
AN-012 AA-005 AG-021 0.0142853 0.102697 0.0271434
AN-11A AA-005 AG-021 0.0213854 0.00321697 0.0301225
AA-005 AU-015 AG-021 0.0465933 2.73041e-09 0.0596402
AA-005 AY-11A AG-021 0.01206 0.0438407 0.0158747
AL-005 AA-005 AG-024 0.044801 2.70136e-07 0.0511633
AL-009 AA-005 AG-024 0.023977 0.00281917 0.0289136
AL-012 AA-005 AG-024 0.049193 2.1783e-05 0.0705451
AL-11B AA-005 AG-024 0.0312794 0.000621826 0.0387853
AN-005 AA-005 AG-024 0.0110001 0.0918827 0.0135677
AN-012 AA-005 AG-024 0.0223264 0.0377361 0.0347522
AN-11A AA-005 AG-024 0.0255481 0.00205358 0.0351005
AA-005 AU-015 AG-024 0.0449744 2.63754e-07 0.0571263
AA-005 AY-11A AG-024 0.00440245 0.295988 0.00581507
AL-009 AL-005 AA-005 0.0232877 9.23059e-05 0.0682551
AL-012 AL-005 AA-005 0.0247185 0.00270555 0.0899492
AL-11B AL-005 AA-005 0.0127965 0.0284922 0.0413915
AL-005 AN-005 AA-005 0.0260936 7.31328e-05 0.0917939
AL-005 AN-012 AA-005 0.00170585 0.42355 0.00687194
AL-005 AN-11A AA-005 0.00306587 0.353769 0.0112233
AL-005 AA-005 AU-015 0.0445497 1.37523e-11 0.079584
AL-005 AA-005 AY-11A 0.0404087 4.05577e-10 0.107462
AL-012 AL-009 AA-005 0.00559366 0.249411 0.0186738
AL-009 AL-11B AA-005 0.00943833 0.0836277 0.0282466
AL-009 AN-005 AA-005 0.0449727 1.5143e-10 0.151414
AL-009 AN-012 AA-005 0.0212273 0.0177264 0.0776913
AL-009 AN-11A AA-005 0.0161655 0.0198343 0.0556357
AL-009 AA-005 AU-015 0.0296078 3.93671e-06 0.0549838
AL-009 AA-005 AY-11A 0.0283722 7.10866e-06 0.0764691
AL-012 AL-11B AA-005 0.0120739 0.100681 0.040606
AL-012 AN-005 AA-005 0.0415108 1.46594e-05 0.160944
AL-012 AN-012 AA-005 0.026553 0.0112257 0.106014
AL-012 AN-11A AA-005 0.0304664 0.00158947 0.115318
AL-012 AA-005 AU-015 0.0515282 4.0209e-08 0.116862
AL-012 AA-005 AY-11A 0.0266531 0.0019639 0.0856786
AL-11B AN-005 AA-005 0.0411586 3.48856e-08 0.144926
AL-11B AN-012 AA-005 0.0153657 0.0587448 0.0584375
AL-11B AN-11A AA-005 0.012616 0.068485 0.0445041
AL-11B AA-005 AU-015 0.0448938 5.24172e-09 0.0843689
AL-11B AA-005 AY-11A 0.0154055 0.0193894 0.0444291
AN-012 AN-005 AA-005 0.0225341 0.0103198 0.0894095
AN-11A AN-005 AA-005 0.0192481 0.00736774 0.0747572
AN-005 AA-005 AU-015 0.0225088 0.000574468 0.0470077
AN-005 AA-005 AY-11A 0.00117311 0.431576 0.00369339
AN-012 AN-11A AA-005 0.00170418 0.429729 0.006409
AN-012 AA-005 AU-015 0.0177948 0.0310707 0.0522132
AA-005 AN-012 AY-11A 0.00766051 0.211002 0.0297696
AN-11A AA-005 AU-015 0.0170178 0.012789 0.037415
AA-005 AN-11A AY-11A 0.0163163 0.0137041 0.0601115
AA-005 AY-11A AU-015 0.0236215 9.96716e-05 0.0484162
AA-012 AA-009 AA-006 0.041143 8.03739e-05 0.113143
AA-015 AA-006 AA-009 0.00336067 0.319109 0.0104588
AA-006 AA-019 AA-009 0.000356629 0.480917 0.000971785
AB-11A AA-009 AA-006 0.0184059 0.00228246 0.0428436
AA-009 AA-006 AG-018 0.0227984 0.00209746 0.0245703
AA-009 AA-006 AG-021 0.0201762 0.00418964 0.0283091
AA-009 AA-006 AG-024 0.0285379 6.55186e-05 0.0392633
AL-005 AA-009 AA-006 0.0900971 0 0.191175
AL-009 AA-009 AA-006 0.0764791 0 0.160797
AL-012 AA-009 AA-006 0.0973866 0 0.220456
AL-11B AA-009 AA-006 0.0990755 0 0.205175
AN-005 AA-009 AA-006 0.0724479 0 0.157125
AN-012 AA-009 AA-006 0.0581615 6.31831e-08 0.153519
AN-11A AA-009 AA-006 0.0668625 7.77156e-16 0.156218
AU-015 AA-006 AA-009 0.0177911 0.00711707 0.0479184
AY-11A AA-009 AA-006 0.0266081 1.65056e-05 0.0643822
AA-006 AA-015 AA-012 0.00249689 0.406509 0.00421334
AA-006 AA-019 AA-012 0.0184735 0.0318985 0.0302149
AA-012 AB-11A AA-006 0.0448856 1.9202e-06 0.112021
AA-012 AA-006 AG-018 0.0546155 7.0248e-06 0.0632715
AA-012 AA-006 AG-021 0.049377 1.93061e-05 0.0947604
AA-012 AA-006 AG-024 0.0468974 0.00019792 0.0759083
AL-005 AA-012 AA-006 0.0363338 0.00151622 0.0802657
AL-009 AA-012 AA-006 0.0137136 0.103405 0.0332654
AL-012 AA-012 AA-006 0.0706096 5.58682e-10 0.148861
AL-11B AA-012 AA-006 0.0544795 5.24904e-07 0.12423
AN-005 AA-012 AA-006 0.0192745 0.0211686 0.0462514
AN-012 AA-012 AA-006 0.025994 0.0146071 0.0607732
AN-11A AA-012 AA-006 0.0177544 0.0524392 0.0431902
AA-006 AU-015 AA-012 0.0186839 0.037981 0.0296728
AA-012 AY-11A AA-006 0.0246594 0.00906915 0.066676
AA-006 AA-019 AA-015 0.0116565 0.0352866 0.0272777
AA-006 AA-015 AB-11A 0.0139152 0.019631 0.0479301
AA-006 AA-015 AG-018 0.0085232 0.14702 0.00925569
AA-006 AA-015 AG-021 0.00702751 0.180949 0.0100911
AA-006 AA-015 AG-024 0.00508936 0.267998 0.00715348
AA-006 AA-015 AL-005 0.0121175 0.0515325 0.0316354
AA-006 AA-015 AL-009 0.0074222 0.149751 0.018599
AA-006 AA-015 AL-012 0.0192087 0.02358 0.029321
AA-006 AA-015 AL-11B 0.0190237 0.00659675 0.0325882
AA-006 AA-015 AN-005 0.0131927 0.0330578 0.0274477
AA-006 AA-015 AN-012 0.00848891 0.207344 0.0159509
AA-006 AA-015 AN-11A 0.00999836 0.11208 0.0178448
AU-015 AA-015 AA-006 0.00540938 0.204752 0.0122609
AA-006 AA-015 AY-11A 0.00936672 0.0988909 0.0293682
AA-006 AA-019 AB-11A 0.0112739 0.0459795 0.0354715
AA-006 AA-019 AG-018 0.0161731 0.0199823 0.0171323
AA-006 AA-019 AG-021 0.0185903 0.00910518 0.0249606
AA-006 AA-019 AG-024 0.00405936 0.309814 0.00523097
AA-006 AA-019 AL-005 0.00202692 0.381992 0.00498328
AA-006 AA-019 AL-009 0.01176 0.0431045 0.027694
AA-006 AA-019 AL-012 0.0089917 0.143273 0.0125634
AA-006 AA-019 AL-11B 0.00486178 0.262318 0.00758078
AA-006 AA-019 AN-005 0.00608812 0.202353 0.011651
AA-006 AA-019 AN-012 0.00944042 0.143975 0.017047
AA-019 AA-006 AN-11A 0.00469985 0.276643 0.00807153
AA-006 AA-019 AU-015 0.017295 0.00577644 0.0396706
AA-006 AA-019 AY-11A 0.00598284 0.187717 0.0171726
AB-11A AA-006 AG-018 0.0216706 0.00207615 0.0223673
AB-11A AA-006 AG-021 0.0177522 0.0121701 0.0233404
AB-11A AA-006 AG-024 0.0220989 0.00347114 0.0294213
AL-005 AB-11A AA-006 0.0736675 0 0.134913
AL-009 AB-11A AA-006 0.0575551 4.44089e-16 0.107295
AL-012 AB-11A AA-006 0.091152 0 0.195732
AL-11B AB-11A AA-006 0.0838148 0 0.155808
AN-005 AB-11A AA-006 0.0525646 2.66631e-12 0.109233
AN-012 AB-11A AA-006 0.051545 1.08213e-07 0.129089
AN-11A AB-11A AA-006 0.054377 4.27036e-12 0.126567
AA-006 AU-015 AB-11A 0.00705601 0.153624 0.0217113
AY-11A AB-11A AA-006 0.00857982 0.090471 0.0191268
AG-018 AG-021 AA-006 0.00978929 0.140947 0.0150575
AG-018 AG-024 AA-006 0.0272213 0.00210562 0.0528457
AL-005 AA-006 AG-018 0.0674441 1.21761e-11 0.0679261
AL-009 AA-006 AG-018 0.0639552 1.38667e-12 0.0641755
AL-012 AA-006 AG-018 0.0791805 2.17042e-10 0.0917965
AL-11B AA-006 AG-018 0.0719368 3.23097e-12 0.0752065
AN-005 AA-006 AG-018 0.0615329 6.66536e-11 0.0668644
AN-012 AA-006 AG-018 0.0603884 9.80763e-07 0.0692324
AN-11A AA-006 AG-018 0.0636474 7.09673e-10 0.070104
AA-006 AU-015 AG-018 0.00577253 0.260413 0.00617509
AY-11A AA-006 AG-018 0.0341417 8.04261e-06 0.0358295
AG-021 AG-024 AA-006 0.0107642 0.131966 0.0220126
AL-005 AA-006 AG-021 0.0710554 1.88738e-15 0.0890215
AL-009 AA-006 AG-021 0.0668681 1.11022e-16 0.0855574
AL-012 AA-006 AG-021 0.0728795 7.60865e-10 0.122681
AL-11B AA-006 AG-021 0.0684274 3.84803e-13 0.0917216
AN-005 AA-006 AG-021 0.064869 3.20499e-12 0.0887718
AN-012 AA-006 AG-021 0.0501532 2.92278e-06 0.0982116
AN-11A AA-006 AG-021 0.0675804 8.0369e-13 0.0983377
AA-006 AU-015 AG-021 0.00607769 0.230076 0.00846194
AY-11A AA-006 AG-021 0.0291728 0.000187538 0.0403829
AL-005 AA-006 AG-024 0.0862161 0 0.103494
AL-009 AA-006 AG-024 0.0668783 6.59695e-13 0.0855212
AL-012 AA-006 AG-024 0.0947539 1.11799e-13 0.139096
AL-11B AA-006 AG-024 0.0719037 4.39981e-13 0.091294
AN-005 AA-006 AG-024 0.0559002 5.74108e-10 0.0727222
AN-012 AA-006 AG-024 0.0627046 4.8201e-06 0.0972947
AN-11A AA-006 AG-024 0.0665442 7.57805e-12 0.0929447
AU-015 AA-006 AG-024 0.00127416 0.443796 0.00172785
AY-11A AA-006 AG-024 0.0404662 2.57947e-06 0.052828
AL-005 AL-009 AA-006 0.0145528 0.0217775 0.025221
AL-012 AL-005 AA-006 0.0179314 0.0371341 0.0349802
AL-11B AL-005 AA-006 0.00854682 0.13124 0.0146319
AL-005 AN-005 AA-006 0.0200231 0.00476821 0.0383604
AL-005 AN-012 AA-006 0.0182297 0.0309185 0.0440485
AL-005 AN-11A AA-006 0.0184974 0.0148746 0.0400773
AA-006 AU-015 AL-005 0.00247541 0.365898 0.00605818
AL-005 AY-11A AA-006 0.0607431 1.4877e-14 0.124471
AL-012 AL-009 AA-006 0.040874 7.78658e-06 0.0794355
AL-11B AL-009 AA-006 0.0244628 0.00124749 0.0413284
AL-009 AN-005 AA-006 8.30252e-05 0.495953 0.000166401
AL-009 AN-012 AA-006 0.00394858 0.365848 0.00978589
AN-11A AL-009 AA-006 0.00242043 0.387395 0.00554679
AA-006 AU-015 AL-009 0.00441365 0.259331 0.0105692
AL-009 AY-11A AA-006 0.0488785 7.09122e-12 0.0993893
AL-012 AL-11B AA-006 0.0147589 0.0702989 0.0268085
AL-012 AN-005 AA-006 0.0407514 6.95853e-05 0.0855707
AL-012 AN-012 AA-006 0.0416664 0.000202489 0.0904475
AL-012 AN-11A AA-006 0.0534657 6.43166e-07 0.114083
AA-006 AU-015 AL-012 0.0214408 0.00998273 0.031904
AL-012 AY-11A AA-006 0.0842804 1.11022e-16 0.180744
AL-11B AN-005 AA-006 0.0327589 2.3041e-05 0.0639193
AL-11B AN-012 AA-006 0.0357425 0.000375479 0.0777917
AL-11B AN-11A AA-006 0.0219515 0.00809997 0.0464462
AA-006 AU-015 AL-11B 0.0140318 0.0433667 0.0227226
AL-11B AY-11A AA-006 0.0739645 0 0.142595
AN-012 AN-005 AA-006 0.00540703 0.286197 0.0127123
AN-005 AN-11A AA-006 0.00348427 0.332036 0.00794059
AA-006 AU-015 AN-005 0.00581233 0.217494 0.0111828
AN-005 AY-11A AA-006 0.0416269 3.3165e-08 0.0919508
AN-012 AN-11A AA-006 0.00164921 0.436483 0.00408205
AA-006 AU-015 AN-012 0.0149457 0.060335 0.0271122
AN-012 AY-11A AA-006 0.0409882 0.000133768 0.105005
AA-006 AU-015 AN-11A 0.00843017 0.162761 0.0147803
AN-11A AY-11A AA-006 0.0370222 3.12945e-06 0.0845475
AA-006 AU-015 AY-11A 0.00439218 0.268926 0.0130672
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AA-012 AL-009 AA-009 0.0124832 0.127733 0.0446271
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AL-012 AA-009 AA-015 0.0768167 3.19744e-14 0.194554
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AA-009 AA-019 AG-021 0.0308905 5.06824e-05 0.0431061
AA-009 AA-019 AG-024 0.0222203 0.00303064 0.0290266
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AL-009 AA-009 AA-019 0.071259 0 0.149588
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AL-009 AA-009 AG-018 0.0447402 2.17444e-08 0.0459912
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AL-009 AA-009 AG-021 0.0464127 1.21997e-08 0.0616316
AL-012 AA-009 AG-021 0.0535183 2.36569e-06 0.0917071
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AN-005 AA-009 AG-021 0.0473082 2.37892e-08 0.0653547
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AL-009 AA-009 AG-024 0.0468012 1.61385e-07 0.0604514
AL-012 AA-009 AG-024 0.0650272 1.27126e-07 0.094976
AL-11B AA-009 AG-024 0.0555789 1.58401e-07 0.0702634
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AA-009 AU-015 AG-024 0.0214147 0.00740655 0.0301071
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AL-012 AL-005 AA-009 0.0109339 0.123075 0.0305524
AL-005 AL-11B AA-009 0.00291762 0.351102 0.00659548
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AL-005 AY-11A AA-009 0.0525244 6.03351e-12 0.124727
AL-012 AL-009 AA-009 0.0455942 2.36052e-07 0.12939
AL-11B AL-009 AA-009 0.039611 9.56478e-08 0.0894811
AN-005 AL-009 AA-009 0.0038687 0.306442 0.00998378
AN-012 AL-009 AA-009 0.00593114 0.279727 0.0210617
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AL-009 AA-009 AU-015 0.0576791 1.22125e-15 0.120847
AL-009 AY-11A AA-009 0.0124873 0.0336195 0.0318779
AL-012 AL-11B AA-009 0.00882983 0.183289 0.0242748
AL-012 AN-005 AA-009 0.0333102 0.00103177 0.0989834
AL-012 AN-012 AA-009 0.0481067 3.55742e-05 0.149706
AL-012 AN-11A AA-009 0.0508784 1.37395e-06 0.16331
AL-012 AA-009 AU-015 0.0725551 5.85565e-12 0.194096
AL-012 AY-11A AA-009 0.0516353 2.33445e-07 0.152989
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AL-11B AN-012 AA-009 0.0295089 0.00321791 0.096885
AL-11B AN-11A AA-009 0.03046 0.000278524 0.08845
AL-11B AA-009 AU-015 0.0704755 8.99281e-15 0.141955
AL-11B AY-11A AA-009 0.0497568 5.42401e-10 0.117729
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AN-012 AN-11A AA-009 0.0110674 0.105714 0.0415557
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AN-012 AY-11A AA-009 0.0140964 0.0856919 0.0552096
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AN-11A AY-11A AA-009 0.0106157 0.0918783 0.0322962
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AA-012 AB-11A AA-015 0.0381184 4.11822e-05 0.100386
AA-012 AA-015 AG-018 0.0493733 0.000319226 0.0577268
AA-012 AA-015 AG-021 0.025578 0.0123796 0.0515872
AA-012 AA-015 AG-024 0.0345496 0.0104117 0.0569847
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AL-009 AA-012 AA-015 0.022252 0.018017 0.0569418
AL-012 AA-012 AA-015 0.0623745 3.19814e-07 0.147634
AL-11B AA-012 AA-015 0.052356 2.39226e-06 0.11789
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AA-012 AY-11A AA-015 0.0195056 0.0280144 0.0534221
AA-012 AB-11A AA-019 0.0360768 0.000185342 0.116455
AA-012 AA-019 AG-018 0.0648632 4.46807e-07 0.0765137
AA-012 AA-019 AG-021 0.0600394 7.76615e-08 0.116405
AA-012 AA-019 AG-024 0.0492393 0.000236052 0.0777047
AL-005 AA-012 AA-019 0.0476942 8.99696e-06 0.121458
AL-009 AA-012 AA-019 0.019495 0.0292058 0.0554969
AL-012 AA-012 AA-019 0.0813164 6.74683e-13 0.197115
AL-11B AA-012 AA-019 0.0682862 6.13183e-09 0.178491
AN-005 AA-012 AA-019 0.0276365 0.00266652 0.0754651
AN-012 AA-012 AA-019 0.0289364 0.00269184 0.084101
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AA-019 AU-015 AA-012 0.00169095 0.430777 0.00292387
AA-012 AY-11A AA-019 0.0158664 0.0617455 0.0509102
AA-012 AB-11A AG-018 0.0415984 0.000162386 0.0463069
AA-012 AB-11A AG-021 0.033501 0.000520361 0.0607218
AA-012 AB-11A AG-024 0.0271195 0.0166192 0.0419062
AL-005 AA-012 AB-11A 0.0535775 1.30367e-07 0.210798
AL-009 AA-012 AB-11A 0.0421628 6.87183e-06 0.174597
AL-012 AA-012 AB-11A 0.0681618 1.21459e-09 0.276082
AL-11B AA-012 AB-11A 0.055143 2.02399e-07 0.21607
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AN-012 AA-012 AB-11A 0.029328 0.00151907 0.145557
AN-11A AA-012 AB-11A 0.0197481 0.0418957 0.100119
AA-012 AB-11A AU-015 0.0244209 0.00480236 0.0770148
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AG-018 AG-024 AA-012 0.0405718 0.00375776 0.0540175
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AL-009 AA-012 AG-018 0.00682364 0.282613 0.00757864
AL-012 AA-012 AG-018 0.0489486 0.000125443 0.0518802
AL-11B AA-012 AG-018 0.0383336 0.00172328 0.0408082
AN-005 AA-012 AG-018 0.0028833 0.395832 0.00325476
AN-012 AA-012 AG-018 0.0239276 0.0467665 0.0260895
AN-11A AA-012 AG-018 0.0247879 0.023729 0.0264949
AA-012 AU-015 AG-018 0.0557281 6.19966e-06 0.0659482
AA-012 AY-11A AG-018 0.0205483 0.0345232 0.0231545
AG-021 AG-024 AA-012 0.00343749 0.363835 0.00519927
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AL-009 AA-012 AG-021 0.0167327 0.0726024 0.0316213
AL-012 AA-012 AG-021 0.047251 0.000143303 0.0863354
AL-11B AA-012 AG-021 0.0391181 0.000503743 0.0705208
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AN-012 AA-012 AG-021 0.0206412 0.029018 0.0412179
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AA-012 AU-015 AG-021 0.046312 5.13007e-05 0.0833987
AA-012 AY-11A AG-021 0.0123917 0.14437 0.023246
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AL-009 AA-012 AG-024 0.0178676 0.0648104 0.0282562
AL-012 AA-012 AG-024 0.0577746 5.41564e-06 0.0815261
AL-11B AA-012 AG-024 0.0373046 0.00223849 0.0543396
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AN-012 AA-012 AG-024 0.0257662 0.0182632 0.0379209
AN-11A AA-012 AG-024 0.0191201 0.052212 0.0291614
AA-012 AU-015 AG-024 0.0371485 0.00142132 0.0580511
AA-012 AY-11A AG-024 0.00652653 0.316191 0.0104608
AL-005 AL-009 AA-012 0.00638329 0.273846 0.00982564
AL-005 AL-012 AA-012 0.0178295 0.0429624 0.0294885
AL-005 AL-11B AA-012 0.0164805 0.0590428 0.0254664
AL-005 AN-005 AA-012 0.0445838 4.95488e-07 0.0717799
AL-005 AN-012 AA-012 0.0704781 4.2108e-10 0.127018
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AL-005 AA-012 AY-11A 0.0644751 1.25829e-09 0.245172
AL-009 AL-012 AA-012 0.0153613 0.0733377 0.0248924
AL-009 AL-11B AA-012 0.00517492 0.319713 0.00810911
AL-009 AN-005 AA-012 0.0380928 6.15331e-05 0.0652293
AL-009 AN-012 AA-012 0.0556839 5.5176e-06 0.102689
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AL-009 AA-012 AU-015 0.0341586 0.00084406 0.104006
AL-009 AA-012 AY-11A 0.0546778 1.04035e-07 0.19639
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AL-012 AN-012 AA-012 0.0489035 0.000227512 0.095745
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AL-012 AA-012 AU-015 0.0712601 1.91645e-09 0.18595
AL-012 AA-012 AY-11A 0.069543 8.9826e-09 0.241675
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AL-11B AN-012 AA-012 0.0481077 2.40363e-05 0.0908604
AL-11B AN-11A AA-012 0.0513008 1.98288e-05 0.0917496
AL-11B AA-012 AU-015 0.066947 8.06372e-09 0.172382
AL-11B AA-012 AY-11A 0.058997 1.67294e-07 0.234509
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AN-012 AA-012 AY-11A 0.0180436 0.0553442 0.0855776
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AN-11A AA-012 AY-11A 0.00695711 0.268953 0.0330673
AA-012 AY-11A AU-015 0.0140069 0.0919577 0.0423785
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AA-015 AA-019 AG-021 0.00745004 0.156682 0.0106085
AA-015 AA-019 AG-024 0.000594631 0.470051 0.000820777
AA-019 AA-015 AL-005 0.0115799 0.0449879 0.0291882
AA-015 AA-019 AL-009 0.00368887 0.300446 0.00917551
AA-019 AA-015 AL-012 0.0070396 0.215826 0.0104468
AA-019 AA-015 AL-11B 0.013475 0.0356552 0.0221092
AA-019 AA-015 AN-005 0.00998745 0.08926 0.0202631
AA-015 AA-019 AN-012 0.000278315 0.488623 0.000538746
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AB-11A AA-015 AG-021 0.0252213 0.00034461 0.0356991
AB-11A AA-015 AG-024 0.0252254 0.000968703 0.034227
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AL-012 AB-11A AA-015 0.0771572 1.44329e-15 0.177539
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AN-012 AB-11A AA-015 0.0440939 6.75322e-06 0.116861
AN-11A AB-11A AA-015 0.0475176 8.2528e-09 0.108283
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AG-018 AG-024 AA-015 0.0282832 0.00080186 0.0601218
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AL-009 AA-015 AG-018 0.0765594 2.22045e-16 0.0793386
AL-012 AA-015 AG-018 0.0835864 8.91509e-13 0.0956858
AL-11B AA-015 AG-018 0.0808688 1.01574e-12 0.0863387
AN-005 AA-015 AG-018 0.0664435 7.89002e-12 0.0731777
AN-012 AA-015 AG-018 0.0656494 2.16024e-07 0.0782097
AN-11A AA-015 AG-018 0.0655428 1.51727e-10 0.0729985
AU-015 AA-015 AG-018 0.0057832 0.197404 0.00588183
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AG-021 AG-024 AA-015 0.0119833 0.102388 0.026281
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AL-009 AA-015 AG-021 0.0716566 0 0.0957837
AL-012 AA-015 AG-021 0.0671516 6.3325e-10 0.112078
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AN-005 AA-015 AG-021 0.0641281 1.7516e-12 0.0920573
AN-012 AA-015 AG-021 0.0361601 0.000562304 0.0725465
AN-11A AA-015 AG-021 0.0623761 2.62116e-09 0.0932073
AA-015 AU-015 AG-021 8.57644e-05 0.495059 0.000116021
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AL-009 AA-015 AG-024 0.0733495 5.68434e-14 0.0948198
AL-012 AA-015 AG-024 0.0822567 8.84959e-12 0.121298
AL-11B AA-015 AG-024 0.0789228 3.33067e-16 0.101877
AN-005 AA-015 AG-024 0.0550626 7.9981e-09 0.0758513
AN-012 AA-015 AG-024 0.048215 8.0213e-05 0.0772413
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AY-11A AA-015 AG-024 0.0428247 1.02327e-06 0.0565267
AL-005 AL-009 AA-015 0.00822236 0.126306 0.014917
AL-012 AL-005 AA-015 0.0191019 0.0298212 0.039811
AL-11B AL-005 AA-015 0.00575825 0.216835 0.0105613
AL-005 AN-005 AA-015 0.020036 0.00474967 0.0392808
AL-005 AN-012 AA-015 0.01429 0.0865426 0.035848
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AL-005 AY-11A AA-015 0.058013 2.22045e-15 0.113225
AL-012 AL-009 AA-015 0.028296 0.00130082 0.0602385
AL-11B AL-009 AA-015 0.0160971 0.017717 0.0276621
AL-009 AN-005 AA-015 0.00670692 0.193412 0.0130697
AL-009 AN-012 AA-015 0.0112084 0.156364 0.0283704
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AU-015 AA-015 AL-009 0.00463606 0.235456 0.0109449
AL-009 AY-11A AA-015 0.0512255 1.31894e-13 0.101564
AL-012 AL-11B AA-015 0.0127505 0.113696 0.0257017
AL-012 AN-005 AA-015 0.029957 0.00136619 0.0661641
AL-012 AN-012 AA-015 0.0420903 0.00012613 0.0994239
AL-012 AN-11A AA-015 0.0476916 2.22478e-06 0.107962
AA-015 AU-015 AL-012 0.00515048 0.263507 0.00736602
AL-012 AY-11A AA-015 0.0697285 3.56049e-13 0.159006
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AL-005 AL-009 AU-015 0.0110326 0.0608114 0.0193519
AL-005 AL-009 AY-11A 0.00615223 0.177892 0.0156661
AL-11B AL-012 AL-005 0.00593735 0.246546 0.0216728
AL-012 AL-005 AN-005 0.0223332 0.0105672 0.055945
AL-005 AL-012 AN-012 0.0251277 0.0121878 0.0531785
AL-005 AL-012 AN-11A 0.0079113 0.223481 0.0170416
AL-012 AL-005 AU-015 0.0155424 0.0562732 0.0346497
AL-005 AL-012 AY-11A 0.000590828 0.476001 0.00186856
AL-11B AL-005 AN-005 0.0106689 0.0778541 0.0226858
AL-005 AL-11B AN-012 0.0294597 0.000651687 0.0567413
AL-005 AL-11B AN-11A 0.0335165 2.89303e-05 0.0607855
AL-11B AL-005 AU-015 0.00493007 0.253692 0.00882826
AL-005 AL-11B AY-11A 0.0201109 0.00168998 0.0548619
AN-012 AN-005 AL-005 0.0231076 0.00562892 0.0778542
AN-11A AN-005 AL-005 0.0121982 0.0613907 0.0392004
AL-005 AN-005 AU-015 0.0191361 0.00742739 0.0373046
AL-005 AN-005 AY-11A 0.0343238 6.25837e-07 0.101872
AN-012 AN-11A AL-005 0.00674776 0.263102 0.0217409
AL-005 AN-012 AU-015 0.0234279 0.0102008 0.0630735
AL-005 AN-012 AY-11A 0.0434382 3.70388e-06 0.156836
AL-005 AN-11A AU-015 0.0216216 0.00522109 0.0452335
AL-005 AN-11A AY-11A 0.054497 9.05154e-12 0.190358
AL-005 AY-11A AU-015 0.0648233 0 0.132047
AL-012 AL-11B AL-009 0.0159555 0.0388086 0.0590613
AL-009 AL-012 AN-005 0.0182528 0.0208853 0.0429699
AL-009 AL-012 AN-012 0.0358963 0.000726253 0.0710962
AL-009 AL-012 AN-11A 0.0195494 0.0331048 0.0388322
AL-012 AL-009 AU-015 0.025389 0.00277313 0.0544553
AL-012 AL-009 AY-11A 0.00479369 0.307503 0.0157826
AL-009 AL-11B AN-005 0.0308284 1.5151e-05 0.0586644
AL-009 AL-11B AN-012 0.0351684 0.000404673 0.0648894
AL-009 AL-11B AN-11A 0.0421741 1.6227e-07 0.0760651
AL-11B AL-009 AU-015 0.0173554 0.0117408 0.029771
AL-009 AL-11B AY-11A 0.0122152 0.0483158 0.0329565
AN-005 AN-012 AL-009 0.0054153 0.282137 0.0144826
AN-005 AN-11A AL-009 0.0177947 0.0127069 0.0469238
AL-009 AN-005 AU-015 0.00479585 0.271472 0.00990868
AL-009 AN-005 AY-11A 0.0234632 0.000960451 0.0736749
AN-012 AN-11A AL-009 0.00863061 0.204046 0.0228157
AL-009 AN-012 AU-015 0.0137861 0.103801 0.038435
AL-009 AN-012 AY-11A 0.0344129 0.00125429 0.125907
AL-009 AN-11A AU-015 0.00202788 0.406018 0.00449439
AL-009 AN-11A AY-11A 0.0427308 4.17899e-08 0.148064
AL-009 AY-11A AU-015 0.0500563 1.42819e-12 0.0987265
AL-012 AL-11B AN-005 0.0101311 0.143208 0.0246308
AL-012 AL-11B AN-012 0.000364073 0.487574 0.000775861
AL-012 AL-11B AN-11A 0.0130061 0.120218 0.0285951
AL-012 AL-11B AU-015 0.0095817 0.171048 0.02055
AL-012 AL-11B AY-11A 0.00655933 0.236235 0.0200142
AN-005 AN-012 AL-012 0.0283546 0.00826296 0.0568181
AN-005 AN-11A AL-012 0.0347858 0.000369417 0.0628265
AL-012 AN-005 AU-015 0.0276486 0.00392428 0.0654882
AL-012 AN-005 AY-11A 0.0214916 0.0138601 0.0728266
AN-11A AN-012 AL-012 0.00453263 0.336894 0.00982554
AL-012 AN-012 AU-015 0.0360473 0.00161908 0.0916795
AL-012 AN-012 AY-11A 0.0453493 0.000137604 0.165603
AL-012 AN-11A AU-015 0.0408299 2.52683e-05 0.096829
AL-012 AN-11A AY-11A 0.0527813 2.61317e-08 0.212927
AL-012 AY-11A AU-015 0.0659443 1.89215e-12 0.156698
AN-005 AN-012 AL-11B 0.019803 0.0302941 0.050247
AN-005 AN-11A AL-11B 0.0253858 0.00114817 0.0542881
AL-11B AN-005 AU-015 0.0222259 0.00298252 0.0446117
AL-11B AN-005 AY-11A 0.0179546 0.0171954 0.0578819
AN-012 AN-11A AL-11B 0.00692496 0.233134 0.0182173
AL-11B AN-012 AU-015 0.0352032 0.000536049 0.0902867
AL-11B AN-012 AY-11A 0.0260191 0.00652857 0.0940366
AL-11B AN-11A AU-015 0.0234578 0.00333341 0.0469938
AL-11B AN-11A AY-11A 0.0348468 2.75222e-05 0.117069
AL-11B AY-11A AU-015 0.0654228 4.44089e-16 0.129954
AN-012 AN-11A AN-005 0.00724035 0.246414 0.0239987
AN-005 AN-012 AU-015 0.00304255 0.374801 0.00823796
AN-005 AN-012 AY-11A 0.00970174 0.168551 0.0387027
AN-005 AN-11A AU-015 0.00529463 0.257529 0.0108195
AN-005 AN-11A AY-11A 0.0260514 0.000451228 0.0963896
AN-005 AY-11A AU-015 0.041224 7.56682e-08 0.0882666
AN-012 AN-11A AU-015 0.000548414 0.477613 0.00154481
AN-012 AN-11A AY-11A 0.0109068 0.129579 0.0491811
AN-012 AY-11A AU-015 0.032069 0.00153093 0.0982367
AN-11A AY-11A AU-015 0.0358611 9.93671e-06 0.0779005
|
Hi Mike Thanks for your patience. A few other people reported similar problems. The reason is: Dtrios just kind of "looks over” the tree to find the arrangement of the trios, whereas Fbranch needs to do a full tree data-structure parsing. So the code is different, and the Fbranch code was less flexible about the format of the input. In your case it was the dashes "-" in the taxon names that caused the trouble. I have made the parser more flexible, so I think it should work with your file and also for people who have blank spaces in the group names. I also added a check for duplicate entries in the trees. This is all in the latest version r38. Milan |
Hi Milan, I've got the same problem with the version 0.4 r38
But my tree is very simple: (Outgroup,((a,b),c),(((d,h),(e,f)),g)); Do you have any suggestions? best, |
I had a problem with full stops (periods) in my names as well. Replacing with underscores fixed the problem. @siberianhigh Try putting the outgroup at the end? |
Hi Milan, I've got the same problem with the version 0.4 r38 Dsuite Fbranch all10qa11qv.nwk out_combined_tree.txt > all10pop_branch.txt best, |
It looks like the brackets around (internalNode1X) might be redundant. Try removing them? |
Thank you for your reply. I have successfully solved this problem.
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主题: Re: [millanek/Dsuite] Error when parsing tree with Fbranch (#22)
It looks like the brackets around (internalNode1X) might be redundant. Try removing them?
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Hi, I met the same problems as you. Could you please tell me how to solve it? Thanks! |
Hi there, I am having the same error as above. ERROR: The tree string could not be parsed correctly! The remaining unparsed tree string is: I do not have any pop name with periods or - , rather 1pop, 2pop. I also tried with new version yet getting same issue. Can someone help ? |
that means your tree string was not correct. you can check carefully tree string. |
I used the tree generated by FastTree just removing branch values. |
So did I, but the tree string generated by FastTree always didn't work for branch. I conducted a NWK file by myself. |
Thank you so much for your reply. I am confused how would you revise/edit tree. (Outgroup,(18pop,((15pop,(17pop,16pop)),(7pop,(6pop,(5pop,(4pop,(3pop,(1pop,2pop)))))),((11pop,(8pop,10pop),((12pop,9pop),(14pop,13pop))))))); PS: I have also tried putting outgroup at the end |
Thank you very much. I removed 19 and it worked. |
Can you try that your |
Hi,
Thanks for creating this package.
I am experiencing a similar issue as posted here (#13), but the solution was not provided:
##Command:
Dsuite Fbranch tree.nwk combined_tree.txt > f_branch.txt
##Error:
ERROR: The tree string could not be parsed correctly! The remaining unparsed tree string is:
(Outgroup,((AG-018,AG-024),((AA-006,AA-019),(AU-015,AA-015))));
I used the same tree file for the Dtrios and DtriosCombine commands and that successfully generated the combined_tree.txt file for the F_branch command. Sub-setting the data and removing the Outgroup didn't make any difference.
Any ideas what could be causing this error?
All the best,
Mike
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