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 key | OTT IDs exemplified |
---|---|
pg_2576@tree5975 | ott246899, ott251774, ott296891, ott486681, ott490378, ott602720, ott872896, ott938556, ott941957, ott976545 |
ot_739@tree1 | ott1074258, ott24769, ott280949, ott358620, ott3638439, ott3638453, ott3638459, ott3638537, ott415032, ott415033, ott415034 |
ot_737@tree1 | ott195559, ott850184 |
pg_1870@tree3769 | ott196433 |
pg_2655@tree6181 | ott338072, ott952934 |
ot_733@tree2 | ott164260, ott164262, ott216167, ott478892, ott559622, ott628709, ott628711, ott738859, ott738861, ott738863, ott738866, ott789561, ott789563 |
pg_2653@tree6178 | ott862685 |
ot_735@tree1 | ott145121, ott186478, ott224059, ott237338, ott237343, ott288451, ott300513, ott308750, ott338836, ott36216, ott447618, ott463419, ott583640, ott583648, ott710014, ott781784, ott837201, ott867524, ott883413 |
pg_2589@tree6001 | ott130462, ott3637837, ott3637905, ott482925, ott514251, ott550034, ott767534, ott806560, ott806561, ott816761 |
pg_2659@tree6195 | ott247371, ott546974, ott753346 |
The following table shows the exemplars for each of the 72 OTT Ids that were exemplified:
higher taxon OTT ID | exemplars used |
---|---|
ott482925 | ott63404 |
ott789563 | ott164265 |
ott251774 | ott251761 |
ott3637837 | ott3637846 |
ott216167 | ott216168 |
ott546974 | ott263079 |
ott36216 | ott65341, 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 |
ott872896 | ott171753 |
ott738859 | ott378641 |
ott816761 | ott190991 |
ott837201 | ott427492, ott478058, ott478073, ott549052, ott877094, ott942673, ott953365, ott1036702, ott1043128 |
ott559622 | ott285141 |
ott288451 | ott5034, ott622499, ott3638583 |
ott415032 | ott70556, ott70561, ott688008, ott916275, ott987399 |
ott237338 | ott191031, ott309989, ott582338, ott1088422 |
ott415033 | ott774211, ott833175 |
ott628711 | ott729098 |
ott976545 | ott816994 |
ott781784 | ott18802, 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 |
ott1074258 | ott143398, ott566698 |
ott164262 | ott164259 |
ott806561 | ott232398 |
ott164260 | ott164257 |
ott308750 | ott53653, ott70546, ott70556, ott70561, ott266387, ott308754, ott308767, ott358610, ott358613, ott411039, ott445132, ott688008, ott774211, ott828095, ott833175, ott833184, ott833188, ott833194, ott833202, ott841211, ott916275, ott987399 |
ott246899 | ott145276 |
ott952934 | ott952936 |
ott338836 | ott82326, ott82335, ott84261, ott134571, ott583633, ott617445, ott1021155, ott1092518 |
ott358620 | ott358621 |
ott486681 | ott349351 |
ott550034 | ott470166 |
ott3638459 | ott828095 |
ott3637905 | ott3637904 |
ott296891 | ott296896 |
ott3638453 | ott70546, ott266387 |
ott247371 | ott247362, ott247363, ott247368, ott247370 |
ott338072 | ott173808 |
ott145121 | ott630161, ott731198, ott774443, ott774449 |
ott463419 | ott989902, ott3642093 |
ott767534 | ott114300 |
ott789561 | ott463673 |
ott806560 | ott805492 |
ott280949 | ott545842, ott665887, ott665891, ott696430, ott984924, ott1039330 |
ott415034 | ott308754, ott308767, ott358610, ott358613, ott411039, ott833184, ott833188, ott833194, ott833202, ott841211 |
ott478892 | ott3621714 |
ott3638439 | ott53653 |
ott300513 | ott418643, ott418648 |
ott186478 | ott12409, 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 |
ott602720 | ott568250 |
ott628709 | ott437387 |
ott738866 | ott444 |
ott24769 | ott24770 |
ott583648 | ott125720, ott226659, ott296896, ott731207, ott771199, ott800800, ott804705, ott816994, ott961790, ott1077892, ott3640974 |
ott883413 | ott67211, ott153494, ott183862, ott191026, ott206083, ott257084, ott261419, ott357212, ott404837, ott408337, ott547448, ott674459, ott712274, ott776754, ott831502, ott883392, ott1019735, ott3640773 |
ott514251 | ott18802 |
ott237343 | ott138803, 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 |
ott862685 | ott135969, ott288063 |
ott583640 | ott60129, ott112532, ott152123, ott286876, ott459854, ott496400, ott583642, ott626640, ott640980, ott690695, ott1087004, ott3630200 |
ott753346 | ott63496 |
ott938556 | ott3638583 |
ott224059 | ott21933, ott170664, ott221336, ott253121, ott913377, ott941257, ott3629866, ott3629916, ott3630103 |
ott3638537 | ott25363, ott188701, ott691687 |
ott867524 | ott219189, ott282319, ott459849, ott586344, ott938557, ott3639579 |
ott490378 | ott5855 |
ott710014 | ott43502, ott130358, ott412912, ott412917, ott528477, ott548120, ott548135, ott652156, ott986392 |
ott738861 | ott634726 |
ott195559 | ott70576 |
ott130462 | ott130463 |
ott850184 | ott937953 |
ott941957 | ott207114 |
ott196433 | ott307762 |
ott447618 | ott191016, ott560560, ott989905, ott3631464 |
ott738863 | ott738867 |