With the newer version of HyPhy, it seems as though how annotated trees are parsed has changed. We should update datamonkey-js job submission to reflect his change.
### Branch sets for RELAX analysis
* Selected 43 branches as the _test_ set: `478488770, 149706207, 664699950, 664699948, Node252, Node250, Node248, 795152647, 724899480, Node259, 109068106, 635116136, 795402852, 795323436, 402864747, Node270, Node268, 795228246, 685533192, 545687090, Node275, Node273, Node267, Node265, Node263, 332224382, 297681450, 426357812, 110832709, 57114123, Node284, Node282, Node280, Node278, Node262, Node258, 296210687, 403256847, Node289, Node287, Node257, Node255, Node247`
* Selected 7 branches as the _reference_ set: `829888493, 831225769, 826351608, Node244, Node242, 640810396, 817317597`
* 353 branches are in the unclassified (nuisance) set: `12054987, 6687226, 700438741, 4027889, 17974228, Node9, 155008488, 38231558, 8671490, 183985969, 54311338, Node18, Node16, Node14, Node12, Node8, 530573866, 591386123, Node23, 884527912, 884527910, Node27, 12667704, 5565637, Node31, 327288995, 884527920, 73666470, 884527918, 884527916, 884527914, Node44, Node42, Node40, Node38, 884527908, 240254682, 602672386, 240254688, Node52, Node50, 884527922, 884527928, 884527924, 884527926, Node59, Node57, Node55, Node49, Node47, Node37, Node35, 884527906, Node34, Node30, Node26, Node22, 59895726, 59895724, Node65, 85720641, 86211179, 86211177, 612053414, Node73, Node71, Node69, 395539363, 38231560, Node77, 52857761, 52221229, 31322956, Node82, Node80, Node76, Node68, Node64, 585696530, 507555013, 507693866, 731236363, 533178379, 512989065, 289629292, Node98, Node96, Node94, Node92, 674074617, 532046007, 14192790, 625289930, Node106, 880974618, 589933402, 568939379, 568939385, 37194856, Node116, Node114, 213579634, 25742620, Node119, Node113, Node111, Node109, Node105, Node103, Node101, Node91, 852759624, 667308135, 562835163, Node125, 83630405, 532067275, Node129, 655819600, 504165095, Node132, Node128, Node124, Node122, Node90, Node88, 586461042, 634888841, Node139, 51101223, 471399281, Node142, Node138, 98956513, 617617805, Node145, Node137, 507667492, 47522990, 560959760, 560917086, 744551514, 743705125, Node159, Node157, Node155, Node153, 594657847, 593762353, 602719153, 466021507, 470597006, Node169, Node167, Node165, Node163, 1905885, 594102812, 555986909, 742236428, Node177, Node175, Node173, 556772617, 548463879, 803253841, Node183, Node181, 295007320, Node180, Node172, Node162, Node152, 591302466, 410952805, Node188, 511834482, 62275622, Node193, 671026532, 62275609, 301755248, Node198, Node196, Node192, 472356891, 73975826, Node201, Node191, Node187, Node151, 284813839, 284813829, 284813843, Node208, Node206, 641724698, 284813833, Node212, 284813841, 254838572, 558123362, 98956515, 554548891, Node222, 584053674, 284813831, 194400541, Node227, Node225, Node221, Node219, Node217, Node215, Node211, Node205, 759111738, 98956505, 586551086, 284813847, Node235, Node233, Node231, 505801345, 507931660, Node238, Node230, Node204, Node150, Node148, Node136, Node241, Node135, Node87, Node85, Node63, Node21, Node7, Node5, 698413180, 729741604, 768405188, 541992323, 529449849, Node299, Node297, Node295, Node293, 723552850, 697870545, Node304, 701343627, 700375237, 154813845, 704335932, 677991594, 727000194, 669286296, Node318, Node316, 675421290, 30408052, 543380551, 30408056, 30408054, Node329, Node327, Node325, 30408060, 734704490, 7981414, 30408058, 734704468, 734704494, 734704476, Node345, Node343, Node341, Node339, Node337, 734704466, 734704474, Node349, 734704478, 734704482, Node352, Node348, Node336, 734704488, 543297617, 115529268, 542185675, Node359, Node357, Node355, Node335, Node333, 30408062, 525028303, 30408064, Node364, Node362, Node332, Node324, 734704496, 734704508, 734704506, 734704502, 734704498, 734704500, Node375, Node373, Node371, Node369, Node367, Node323, Node321, Node315, Node313, Node311, Node309, Node307, Node303, 694850140, 697033715, 699660929, 696987556, Node384, Node382, Node380, 686608688, Node379, 45382143, 704289124, Node388, Node378, Node302, Node292, Node4, 296142098, 296142096, 296142094, Node394, Node392, 701322822, 2894432, 570517896, 296142092, Node401, Node399, Node397, Node391, Node3`