Error when parsing tree with Fbranch

[mrml500]

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

[millanek]

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

[mrml500]

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 — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#22 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALZQMI5QSKSZIMRCIGF75JLR5BPARANCNFSM4PDWW4XA> .

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 AA-012 AA-009 AA-015 0.0256033 0.0058757 0.0703075 AA-012 AA-009 AA-019 0.0337913 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1.00253e-13 0.0946021 AL-11B AY-11A AG-021 0.0375092 1.26556e-05 0.0489802 AN-005 AN-012 AG-021 0.00413576 0.337656 0.00754799 AN-11A AN-005 AG-021 0.00496017 0.295287 0.00696892 AN-005 AU-015 AG-021 0.0682718 3.20743e-13 0.0932814 AN-005 AY-11A AG-021 0.0311396 0.000102029 0.0427309 AN-11A AN-012 AG-021 0.00210936 0.425368 0.00359752 AN-012 AU-015 AG-021 0.0512642 6.26385e-07 0.102272 AN-012 AY-11A AG-021 0.0269212 0.00964049 0.0568761 AN-11A AU-015 AG-021 0.0654753 1.22043e-10 0.0973674 AN-11A AY-11A AG-021 0.0298848 0.000308279 0.0427251 AY-11A AU-015 AG-021 0.0340143 3.24667e-05 0.0472526 AL-005 AL-009 AG-024 0.0198639 0.0181464 0.0223512 AL-012 AL-005 AG-024 0.0131112 0.1282 0.0170703 AL-005 AL-11B AG-024 0.015756 0.0306914 0.017976 AL-005 AN-005 AG-024 0.0344459 8.07728e-05 0.0403782 AL-005 AN-012 AG-024 0.0195376 0.0647651 0.0282806 AL-005 AN-11A AG-024 0.0174613 0.0542348 0.0227863 AL-005 AU-015 AG-024 0.0832968 0 0.100021 AL-005 AY-11A AG-024 0.0454921 4.07873e-07 0.0554485 AL-012 AL-009 AG-024 0.0346267 0.00089365 0.0448309 AL-11B AL-009 AG-024 0.00470703 0.298876 0.00527937 AL-009 AN-005 AG-024 0.0149392 0.0705425 0.0188732 AN-012 AL-009 AG-024 0.000654537 0.480619 0.00100013 AN-11A AL-009 AG-024 0.00381373 0.350044 0.00509664 AL-009 AU-015 AG-024 0.0648007 5.08518e-11 0.0826867 AL-009 AY-11A AG-024 0.0251285 0.00442134 0.031943 AL-012 AL-11B AG-024 0.026947 0.00788351 0.0334588 AL-012 AN-005 AG-024 0.0428159 0.000224219 0.0589592 AL-012 AN-012 AG-024 0.0287165 0.0296792 0.0400187 AL-012 AN-11A AG-024 0.0356405 0.00316018 0.0503606 AL-012 AU-015 AG-024 0.0876745 1.22446e-12 0.124156 AL-012 AY-11A AG-024 0.0565381 2.20052e-06 0.0774331 AL-11B AN-005 AG-024 0.0240876 0.00508062 0.0307469 AL-11B AN-012 AG-024 0.016184 0.0668619 0.0238381 AL-11B AN-11A AG-024 0.0100787 0.171743 0.0131404 AL-11B AU-015 AG-024 0.0686314 5.15114e-11 0.0888364 AL-11B AY-11A AG-024 0.0364315 0.000174953 0.0452359 AN-012 AN-005 AG-024 0.0126215 0.120179 0.0183788 AN-11A AN-005 AG-024 0.0108705 0.148198 0.0145206 AN-005 AU-015 AG-024 0.054405 2.07127e-09 0.0757458 AN-005 AY-11A AG-024 0.0172552 0.0311221 0.0229302 AN-012 AN-11A AG-024 0.00201567 0.439036 0.00270258 AN-012 AU-015 AG-024 0.0526158 2.39908e-05 0.0841799 AN-012 AY-11A AG-024 0.02588 0.0314359 0.0398818 AN-11A AU-015 AG-024 0.0575002 4.82143e-07 0.0810214 AN-11A AY-11A AG-024 0.0218621 0.0109517 0.0280213 AY-11A AU-015 AG-024 0.0396108 2.21169e-05 0.0522316 AL-005 AL-009 AL-012 0.0202154 0.0161301 0.0402741 AL-005 AL-009 AL-11B 0.0406949 6.60785e-09 0.0822725 AL-009 AL-005 AN-005 0.0415644 1.51351e-09 0.0829195 AL-009 AL-005 AN-012 0.00580117 0.28083 0.0117757 AL-009 AL-005 AN-11A 0.00762391 0.15018 0.0139293 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

[millanek]

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

[siberianhigh]

Hi Milan,

I've got the same problem with the version 0.4 r38

Dsuite Fbranch tree.txt sets__tree.txt > fbranch.txt ERROR: The tree string could not be parsed correctly! The remaining unparsed tree string is: (Outgroup,internalNode1X,internalNode5X);

But my tree is very simple: (Outgroup,((a,b),c),(((d,h),(e,f)),g));

Do you have any suggestions?

best,
Evgeniy

[SethMusker]

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?
(((a,b),c),(((d,h),(e,f)),g),Outgroup);

[furr-rui]

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
ERROR: The tree string could not be parsed correctly! The remaining unparsed tree string is:
(((((((internalNode0X,(internalNode1X)),TBS),internalNode4X),JJL),DWX),internalNode13X),Outgroup);
Do you have any suggestions?

best,
frr

[SethMusker]

It looks like the brackets around (internalNode1X) might be redundant. Try removing them?

[furr-rui]

Thank you for your reply. I have successfully solved this problem.

…

------------------&nbsp;原始邮件&nbsp;------------------ 发件人: "millanek/Dsuite" ***@***.***&gt;; 发送时间:&nbsp;2022年1月12日(星期三) 下午4:16 ***@***.***&gt;; ***@***.******@***.***&gt;; 主题:&nbsp;Re: [millanek/Dsuite] Error when parsing tree with Fbranch (#22) It looks like the brackets around (internalNode1X) might be redundant. Try removing them? — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you commented.Message ID: ***@***.***&gt;

[yefanglee]

Thank you for your reply. I have successfully solved this problem.
…
------------------ 原始邮件 ------------------ 发件人: "millanek/Dsuite" @.>; 发送时间: 2022年1月12日(星期三) 下午4:16 @.>; @.@.>; 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? — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you commented.Message ID: @.***>

Hi, I met the same problems as you. Could you please tell me how to solve it? Thanks!
((((((internalNode0X)))),(internalNode1X,((NUB),((SIB))))),((FAL.00099760),((BEZ),((WAS,((EUR),((SAF),(EAF,(NAF))))),((SAS),(SC,(NC)))))))

[Prashantevo]

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:
((Dpop,(internalNode1X,internalNode7X,(11pop,internalNode8X,internalNode11X))),Outgroup);

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 ?

[yefanglee]

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: ((Dpop,(internalNode1X,internalNode7X,(11pop,internalNode8X,internalNode11X))),Outgroup);

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.

[Prashantevo]

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: ((Dpop,(internalNode1X,internalNode7X,(11pop,internalNode8X,internalNode11X))),Outgroup);
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.

[yefanglee]

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: ((Dpop,(internalNode1X,internalNode7X,(11pop,internalNode8X,internalNode11X))),Outgroup);
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.

[Prashantevo]

Thank you so much for your reply.

I am confused how would you revise/edit tree.
my tree looks like this:

(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

[yefanglee]

Thank you so much for your reply.

I am confused how would you revise/edit tree. my tree looks like this:

(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

your original tree was showed in below according to your tree string. But I think there was something wrong with it.

Here I reconstructed a tree string: (((((((((((1,2),3),4),5),6),7),((((9,12),(13,14)),(8,10)),11)),((16,17),15)),19),O). I am not sure if it can success in Franch.

[Prashantevo]

Thank you very much. I removed 19 and it worked.

[HuTaoJiaZiAckerman]

Can you try that your tree.nek file put on itol(https://itol.embl.de/) websites to re-root. After export again as a nwk format, you code will work! I hope this approach can slove the problem.