Propinquity output documentation. The top-level docs are here.

The exemplified_phylo directory holds the results of the last step of the input preprocessing for the supertree pipeline. All of the leaves in these trees are mapped to terminal taxa in the taxonomy. This is accomplished by taking the cleaned input trees (see ../cleaned_phylo/index.html and ../cleaned_ott/index.html) and choosing exemplar taxa to represent at for each tip that is mapped to a non-terminal taxon. See for details on the procedure.

Next step: Decomposition of inputs into subproblems. See ../subproblems/index.html for details.

Results: Below you will find tabular or itemized listings of:

Exemplified tree files:

The following source input trees were affected by the exemplar step:

study_id + tree_id keyOTT IDs exemplified
pg_2576@tree5975ott246899, ott251774, ott296891, ott486681, ott490378, ott602720, ott872896, ott938556, ott941957, ott976545
ot_739@tree1ott1074258, ott24769, ott280949, ott358620, ott3638439, ott3638453, ott3638459, ott3638537, ott415032, ott415033, ott415034
ot_737@tree1ott195559, ott850184
pg_1870@tree3769ott196433
pg_2655@tree6181ott338072, ott952934
ot_733@tree2ott164260, ott164262, ott216167, ott478892, ott559622, ott628709, ott628711, ott738859, ott738861, ott738863, ott738866, ott789561, ott789563
pg_2653@tree6178ott862685
ot_735@tree1ott145121, ott186478, ott224059, ott237338, ott237343, ott288451, ott300513, ott308750, ott338836, ott36216, ott447618, ott463419, ott583640, ott583648, ott710014, ott781784, ott837201, ott867524, ott883413
pg_2589@tree6001ott130462, ott3637837, ott3637905, ott482925, ott514251, ott550034, ott767534, ott806560, ott806561, ott816761
pg_2659@tree6195ott247371, ott546974, ott753346

The following table shows the exemplars for each of the 72 OTT Ids that were exemplified:

higher taxon OTT IDexemplars used
ott482925ott63404
ott789563ott164265
ott251774ott251761
ott3637837ott3637846
ott216167ott216168
ott546974ott263079
ott36216ott65341, ott85761, ott95335, ott95340, ott96314, ott107042, ott111652, ott135140, ott135908, ott145257, ott166940, ott166944, ott177748, ott177756, ott179259, ott191033, ott229214, ott234922, ott254734, ott255700, ott333706, ott350980, ott364286, ott383030, ott421135, ott421144, ott425101, ott425111, ott431488, ott457786, ott465396, ott475577, ott484077, ott484093, ott544457, ott564277, ott662022, ott669607, ott713816, ott758985, ott769903, ott792164, ott793159, ott891834, ott891841, ott891845, ott891849, ott893584, ott919140, ott959203, ott959206, ott959219, ott1051956, ott1060673, ott1060680, ott1068742, ott1085993, ott3631235, ott3631369, ott3631389, ott3631390, ott3631396
ott872896ott171753
ott738859ott378641
ott816761ott190991
ott837201ott427492, ott478058, ott478073, ott549052, ott877094, ott942673, ott953365, ott1036702, ott1043128
ott559622ott285141
ott288451ott5034, ott622499, ott3638583
ott415032ott70556, ott70561, ott688008, ott916275, ott987399
ott237338ott191031, ott309989, ott582338, ott1088422
ott415033ott774211, ott833175
ott628711ott729098
ott976545ott816994
ott781784ott18802, ott37552, ott47553, ott63404, ott65145, ott65158, ott92013, ott98391, ott99415, ott100808, ott114300, ott126883, ott126890, ott130458, ott130463, ott132265, ott147741, ott172060, ott190991, ott193341, ott197586, ott209112, ott209116, ott221160, ott230857, ott232398, ott232409, ott244387, ott244398, ott244403, ott248678, ott248681, ott248687, ott263548, ott267494, ott267498, ott267513, ott272138, ott279775, ott282688, ott282691, ott282697, ott284775, ott284782, ott284790, ott286307, ott308746, ott318802, ott318824, ott329865, ott331701, ott377971, ott387080, ott403046, ott415147, ott423838, ott423857, ott427208, ott458077, ott496714, ott496720, ott518755, ott520382, ott542639, ott588670, ott589336, ott614390, ott617146, ott617176, ott618747, ott622927, ott637893, ott638357, ott638366, ott641698, ott641705, ott652031, ott652242, ott700977, ott705124, ott705150, ott721197, ott721208, ott721221, ott721226, ott725183, ott757202, ott770144, ott771615, ott787941, ott790859, ott793086, ott793100, ott805492, ott806535, ott808021, ott815600, ott819087, ott839770, ott845759, ott861020, ott868318, ott898391, ott898400, ott905442, ott910775, ott919831, ott920013, ott963702, ott970988, ott974899, ott974910, ott978520, ott1007866, ott1012144, ott1014036, ott1029429, ott1031380, ott1047782, ott1050227, ott1054955, ott1054967, ott1074010, ott1074011, ott1088696, ott3636901, ott3636957, ott3636960, ott3637010, ott3637017, ott3637039, ott3637116, ott3637120, ott3637121, ott3637124, ott3637192, ott3637201, ott3637241, ott3637258, ott3637264, ott3637275, ott3637332, ott3637393, ott3637446, ott3637455, ott3637459, ott3637470, ott3637501, ott3637547, ott3637562, ott3637571, ott3637575, ott3637601, ott3637682, ott3637787, ott3637826, ott3637844, ott3637846, ott3637872, ott3637904, ott3637910, ott3637916, ott3637955, ott3637994, ott3638035, ott3638074, ott3638086, ott3638088, ott3638089, ott3638090, ott3638103, ott3638115, ott3638116, ott3638124, ott3638136, ott3638191, ott3638207, ott3638210, ott3638233, ott3638239, ott3638366, ott3638377, ott3640053
ott1074258ott143398, ott566698
ott164262ott164259
ott806561ott232398
ott164260ott164257
ott308750ott53653, ott70546, ott70556, ott70561, ott266387, ott308754, ott308767, ott358610, ott358613, ott411039, ott445132, ott688008, ott774211, ott828095, ott833175, ott833184, ott833188, ott833194, ott833202, ott841211, ott916275, ott987399
ott246899ott145276
ott952934ott952936
ott338836ott82326, ott82335, ott84261, ott134571, ott583633, ott617445, ott1021155, ott1092518
ott358620ott358621
ott486681ott349351
ott550034ott470166
ott3638459ott828095
ott3637905ott3637904
ott296891ott296896
ott3638453ott70546, ott266387
ott247371ott247362, ott247363, ott247368, ott247370
ott338072ott173808
ott145121ott630161, ott731198, ott774443, ott774449
ott463419ott989902, ott3642093
ott767534ott114300
ott789561ott463673
ott806560ott805492
ott280949ott545842, ott665887, ott665891, ott696430, ott984924, ott1039330
ott415034ott308754, ott308767, ott358610, ott358613, ott411039, ott833184, ott833188, ott833194, ott833202, ott841211
ott478892ott3621714
ott3638439ott53653
ott300513ott418643, ott418648
ott186478ott12409, ott25005, ott26366, ott26375, ott39821, ott84222, ott84336, ott96976, ott96979, ott96982, ott96985, ott96988, ott96991, ott96994, ott96997, ott97000, ott97004, ott104319, ott137378, ott138316, ott150573, ott150578, ott150583, ott150610, ott152326, ott152341, ott152343, ott170650, ott170654, ott170657, ott177439, ott177443, ott177446, ott177451, ott177455, ott177460, ott177463, ott177466, ott177471, ott186474, ott204908, ott206192, ott208145, ott208154, ott208734, ott209245, ott209250, ott228488, ott228491, ott228502, ott228508, ott228511, ott232890, ott262631, ott262644, ott262648, ott275986, ott283682, ott317218, ott322388, ott322391, ott322394, ott322397, ott322401, ott322405, ott322408, ott322411, ott322415, ott336737, ott339692, ott339695, ott339710, ott339721, ott340808, ott340811, ott340825, ott340829, ott340833, ott340836, ott340842, ott340845, ott350986, ott350989, ott350993, ott350997, ott367806, ott378445, ott378455, ott382470, ott390059, ott390063, ott390358, ott390362, ott390375, ott399802, ott399805, ott399810, ott399830, ott412207, ott422649, ott422653, ott422657, ott422662, ott432908, ott451605, ott451610, ott470346, ott470349, ott474824, ott485055, ott566468, ott566471, ott566478, ott570638, ott585088, ott604412, ott617256, ott618509, ott618512, ott618515, ott618518, ott618521, ott618526, ott618531, ott618534, ott618537, ott675425, ott748108, ott748112, ott748124, ott748128, ott751773, ott751779, ott751784, ott751788, ott751793, ott751796, ott751800, ott751803, ott751807, ott751811, ott790831, ott790866, ott790884, ott802521, ott802525, ott814721, ott814726, ott846801, ott846810, ott846813, ott846816, ott846819, ott846824, ott848582, ott848586, ott848589, ott848624, ott865481, ott865485, ott865492, ott865495, ott865500, ott865503, ott865507, ott870843, ott875056, ott875061, ott892758, ott892763, ott892766, ott896985, ott896993, ott896996, ott897003, ott897009, ott897598, ott910804, ott915550, ott915659, ott915663, ott919572, ott930912, ott930919, ott930926, ott943011, ott948317, ott948321, ott948325, ott948330, ott948334, ott948338, ott951883, ott951887, ott951892, ott957687, ott957690, ott958706, ott958709, ott958715, ott958718, ott958724, ott961038, ott983421, ott996888, ott996894, ott1002460, ott1004127, ott1009543, ott1009551, ott1009554, ott1012106, ott1012110, ott1012113, ott1028738, ott1028741, ott1046578, ott1095369, ott1095374
ott602720ott568250
ott628709ott437387
ott738866ott444
ott24769ott24770
ott583648ott125720, ott226659, ott296896, ott731207, ott771199, ott800800, ott804705, ott816994, ott961790, ott1077892, ott3640974
ott883413ott67211, ott153494, ott183862, ott191026, ott206083, ott257084, ott261419, ott357212, ott404837, ott408337, ott547448, ott674459, ott712274, ott776754, ott831502, ott883392, ott1019735, ott3640773
ott514251ott18802
ott237343ott138803, ott150932, ott178071, ott196516, ott197410, ott237344, ott258651, ott293855, ott300553, ott401066, ott441856, ott466859, ott520272, ott525452, ott568675, ott590742, ott591249, ott591259, ott706144, ott786351, ott874781, ott883978, ott971456, ott979303, ott1009635, ott1084057, ott1084067, ott1098784, ott3632142, ott3632878
ott862685ott135969, ott288063
ott583640ott60129, ott112532, ott152123, ott286876, ott459854, ott496400, ott583642, ott626640, ott640980, ott690695, ott1087004, ott3630200
ott753346ott63496
ott938556ott3638583
ott224059ott21933, ott170664, ott221336, ott253121, ott913377, ott941257, ott3629866, ott3629916, ott3630103
ott3638537ott25363, ott188701, ott691687
ott867524ott219189, ott282319, ott459849, ott586344, ott938557, ott3639579
ott490378ott5855
ott710014ott43502, ott130358, ott412912, ott412917, ott528477, ott548120, ott548135, ott652156, ott986392
ott738861ott634726
ott195559ott70576
ott130462ott130463
ott850184ott937953
ott941957ott207114
ott196433ott307762
ott447618ott191016, ott560560, ott989905, ott3631464
ott738863ott738867