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

The cleaned_phylo contains the results of pruning problematically mapped tips from phylogenetic inputs. Full documentation of the procedure and artifacts can be found in the README. Note that trees in this directory may have tips that are mapped to higher (non-terminal) taxa in the OpenTreeTaxonomy.

Next step: The next step in phylogeny processing is to choose exemplars for tips that are mapped to higher taxa (see ../exemplified_phylo/index.html). First, though, we pre-process the Open Tree Taxonomy (see ../cleaned_ott/index.html).

Results: There were 769 nonempty trees after cleaning. The files of interest in this directory are:

JSON log of pruningpruned newick
ot_895@tree2.json
ot_895@tree1.json
ot_519@tree2.json
ot_519@Tr88326.json
ot_896@tree1.json
pg_1951@tree3975.json
ot_930@tree3.json
pg_1951@tree3974.json
ot_932@tree6.json
ot_942@Tr94692.json
ot_929@tree1.json
pg_1786@tree6257.json
ot_924@Tr97534.json
pg_1761@tree6151.json
pg_2445@tree5206.json
ot_938@tree1.json
pg_1785@tree6248.json
ot_714@tree2.json
ot_944@tree1.json
pg_1788@tree6534.json
ot_957@tree1.json
ot_729@Tr90969.json
ot_949@tree1.json

NO TREE (empty after cleaning)

ot_933@tree2.json
ot_947@tree1.json
ot_954@tree1.json
ot_947@tree3.json
ot_981@tree1.json
ot_947@tree2.json
pg_1947@tree3965.json
ot_925@tree1.json
ot_960@tree1.json
ot_956@tree1.json
ot_900@tree1.json
ot_984@tree1.json
ot_985@tree1.json
ot_983@tree1.json

NO TREE (empty after cleaning)

ot_898@tree1.json
ot_898@tree3.json
ot_898@tree2.json
ot_982@tree4.json
ot_989@tree1.json
ot_990@tree2.json
ot_964@tree2.json
ot_965@tree1.json
ot_523@tree1.json
ot_771@tree1.json
ot_948@tree2.json
ot_951@tree1.json

NO TREE (empty after cleaning)

ot_935@tree2.json

NO TREE (empty after cleaning)

ot_934@tree1.json
ot_613@tree1.json
ot_955@tree1.json
ot_952@tree1.json
ot_987@tree1.json
ot_988@tree1.json
pg_2651@tree6177.json
pg_793@tree5659.json
ot_490@Tr70734.json
pg_406@tree509.json
pg_401@tree5569.json
pg_2466@tree5304.json
ot_497@Tr4479.json
pg_432@tree546.json
ot_372@Tr60567.json
pg_300@tree217.json
ot_408@Tr65494.json
pg_745@tree1360.json

NO TREE (empty after cleaning)

pg_1753@tree3531.json
pg_518@tree733.json
pg_531@tree763.json
pg_485@tree651.json
pg_381@tree448.json
ot_393@Tr72538.json
pg_2486@tree5347.json
ot_467@Tr86931.json
ot_436@Tr70613.json
pg_2697@tree6262.json
pg_2481@tree5339.json
ot_374@Tr61050.json
ot_235@Tr50560.json
pg_2467@tree6025.json
ot_344@Tr60495.json
ot_381@Tr62023.json
pg_1288@tree2584.json
pg_647@tree5621.json
pg_1618@tree5896.json
pg_1328@tree5855.json
pg_2280@tree4827.json
pg_1420@tree5303.json
pg_644@tree1127.json
pg_529@tree761.json
pg_698@tree5648.json
pg_516@tree728.json
pg_1052@tree5770.json
pg_1608@tree5892.json
pg_2518@tree5428.json
pg_860@tree1654.json
pg_699@tree1258.json
pg_2276@tree4823.json
pg_857@tree1651.json
pg_487@tree5599.json
pg_492@tree664.json
pg_1032@tree1981.json
pg_2314@tree4883.json
pg_467@tree5592.json
pg_1631@tree3297.json
pg_2238@tree4729.json
pg_740@tree1346.json
ot_486@Tr2898.json
pg_463@tree604.json
pg_2468@tree5310.json
pg_674@tree1207.json
pg_443@tree562.json
pg_2196@tree4650.json
pg_2206@tree4667.json
pg_776@tree5653.json
pg_404@tree506.json
pg_415@tree5572.json
pg_2300@tree4862.json
pg_1604@tree5891.json
pg_388@tree469.json
pg_668@tree1193.json
pg_361@tree5551.json
pg_2263@tree4797.json

NO TREE (empty after cleaning)

pg_1165@tree2355.json
pg_340@tree5532.json
pg_352@tree388.json
pg_874@tree5717.json
pg_2531@tree5449.json
pg_252@tree211.json

NO TREE (empty after cleaning)

pg_733@tree1324.json
pg_1718@tree3460.json
pg_1719@tree3462.json

NO TREE (empty after cleaning)

pg_525@tree743.json
pg_961@tree5754.json
pg_1177@tree5811.json
pg_1758@tree5940.json
pg_2290@tree4850.json
pg_1757@tree3539.json
pg_1691@tree3407.json
pg_1727@tree3475.json
pg_2222@tree4697.json
pg_1666@tree5901.json
pg_1669@tree5902.json
pg_1678@tree3382.json
pg_1667@tree3362.json
pg_1609@tree3245.json
ot_353@Tr55240.json
pg_1617@tree3261.json
pg_1708@tree3445.json
pg_883@tree1703.json
ot_645@tree1.json
ot_651@tree2.json
pg_2919@tree6749.json
ot_619@tree8.json
ot_75@tree1.json
ot_98@tree1.json
ot_632@tree2.json
ot_620@tree1.json
ot_163@tree1.json
ot_644@tree1.json
ot_640@tree1.json
ot_643@tree1.json
pg_2921@tree6749.json
pg_2923@tree6751.json
ot_646@tree1.json
ot_71@tree1.json
pg_2922@tree6752.json
ot_652@tree4.json
ot_639@tree1.json
ot_74@tree1.json
ot_615@Tr76459.json
ot_634@tree1.json
ot_618@tree1.json
pg_2917@tree6745.json
pg_2918@tree6755.json
pg_2842@tree6603.json
ot_656@tree2.json
ot_813@tree1.json
pg_2827@tree6577.json
pg_761@tree1415.json
pg_77@tree5878.json
pg_754@tree1392.json
pg_330@tree325.json
pg_1131@tree2265.json
pg_2608@tree6288.json
pg_2539@tree6294.json
pg_2645@tree6165.json
pg_2644@tree6164.json
pg_2642@tree6161.json
pg_2626@tree6142.json
pg_332@tree333.json
pg_2832@tree6586.json
pg_1866@tree3765.json
pg_59@tree5731.json
pg_704@tree1266.json
pg_2638@tree6157.json
pg_1974@tree4038.json
pg_1974@tree4039.json
pg_2901@tree6721.json
pg_2906@tree6730.json
pg_1524@tree3046.json
pg_1414@tree2837.json
pg_1411@tree5110.json
pg_1409@tree2822.json
pg_1408@tree2821.json
pg_1407@tree2818.json
pg_1401@tree2812.json
pg_1391@tree2795.json
pg_1434@tree2876.json
pg_2633@tree6153.json
pg_1539@tree3088.json
pg_2634@tree6154.json
pg_1022@tree1967.json
pg_562@tree817.json
pg_588@tree878.json
pg_2048@tree4220.json
pg_1137@tree2295.json
pg_62@tree2878.json
pg_2841@tree6597.json
pg_2085@tree4317.json
pg_180@tree794.json
pg_576@tree849.json
pg_581@tree859.json
pg_582@tree862.json
pg_598@tree926.json
pg_599@tree927.json
pg_603@tree940.json
pg_721@tree1298.json
pg_723@tree1300.json
pg_921@tree4103.json
pg_61@tree816.json
pg_573@tree839.json
pg_566@tree832.json
pg_1522@tree3044.json
pg_1570@tree3142.json
pg_1583@tree3194.json
pg_1572@tree3145.json
pg_2909@tree6735.json
pg_43@tree3862.json
pg_38@tree1750.json
pg_2878@tree6673.json
pg_2624@tree6139.json
pg_2128@tree4437.json
pg_1102@tree2177.json
pg_1129@tree2251.json
pg_1109@tree2201.json
pg_2004@tree4118.json
pg_53@tree1280.json
pg_1118@tree2226.json
pg_2669@tree6213.json
pg_2032@tree5922.json
pg_1901@tree3877.json
pg_713@tree1287.json
pg_2912@tree6740.json
pg_259@tree142.json
pg_264@tree150.json
pg_267@tree161.json
pg_2077@tree4291.json
pg_293@tree201.json
pg_197@tree784.json
pg_595@tree896.json
pg_131@tree6236.json
pg_2689@tree6241.json
pg_597@tree906.json
pg_2001@tree4100.json
pg_606@tree5290.json
pg_270@tree159.json
pg_596@tree901.json
pg_294@tree202.json
pg_292@tree199.json
pg_58@tree775.json
pg_548@tree798.json
pg_2055@tree4234.json
pg_2057@tree4240.json
pg_2127@tree4426.json
pg_594@tree890.json
pg_261@tree145.json
pg_57@tree777.json
pg_1087@tree2114.json
pg_1087@tree2115.json
pg_2690@tree6243.json
pg_2045@tree4213.json
pg_605@tree947.json
pg_271@tree5017.json
pg_2661@tree6198.json
pg_2052@tree4228.json
pg_1103@tree2178.json
pg_14@tree12.json
pg_2598@tree6020.json
pg_2000@tree4098.json
pg_20@tree2162.json
pg_1101@tree2172.json
pg_2565@tree5708.json
pg_1094@tree2138.json
pg_2641@tree6160.json
pg_99@tree5885.json
pg_93@tree1411.json
pg_898@tree1732.json
pg_216@tree5865.json
pg_901@tree1740.json
pg_2830@tree6583.json
pg_2831@tree6584.json
pg_719@tree1296.json
pg_1975@tree4041.json
pg_1821@tree3678.json
pg_1581@tree3188.json
pg_1575@tree3164.json
pg_1573@tree3144.json
pg_934@tree1832.json
pg_200@tree6585.json
pg_152@tree5743.json
pg_53@tree1281.json
pg_2076@tree4282.json
pg_50@tree1397.json
pg_80@tree5881.json
pg_424@tree532.json
pg_82@tree5792.json
pg_1962@tree6580.json
pg_915@tree1802.json
pg_32@tree1775.json
pg_915@tree1803.json
pg_2625@tree6140.json
pg_1130@tree2258.json
pg_2047@tree4217.json
pg_386@tree459.json
pg_139@tree5860.json
pg_126@tree2233.json
pg_136@tree5857.json
pg_1944@tree3959.json
pg_2828@tree6578.json
pg_142@tree38.json
pg_21@tree37.json
pg_75@tree1743.json
pg_41@tree1396.json
pg_2044@tree4212.json
pg_1916@tree3902.json
pg_926@tree1825.json
pg_1133@tree5647.json
pg_625@tree1016.json
pg_1842@tree3724.json
pg_288@tree5028.json
pg_385@tree458.json
pg_1843@tree3725.json
pg_1858@tree3754.json
pg_394@tree483.json
pg_52@tree463.json
pg_2712@tree6296.json
pg_2610@tree6117.json
pg_650@tree1147.json
pg_275@tree167.json
pg_37@tree5871.json
pg_73@tree5787.json
pg_88@tree5848.json
pg_72@tree801.json
pg_283@tree184.json
pg_30@tree2281.json
pg_1443@tree2917.json
pg_2140@tree4483.json
pg_2820@tree6566.json
pg_1483@tree2983.json
pg_1478@tree2974.json
pg_1474@tree2969.json
pg_1473@tree2967.json
pg_1453@tree2932.json
pg_1450@tree2926.json
pg_1384@tree2766.json
pg_1382@tree2763.json
pg_1318@tree2634.json
pg_1312@tree2628.json
pg_2165@tree4564.json
pg_1518@tree6333.json
pg_2898@tree6713.json
pg_2896@tree6709.json
pg_1264@tree2544.json
pg_56@tree5821.json
pg_2648@tree6171.json
pg_2564@tree5699.json
pg_81@tree5863.json
pg_1996@tree4089.json
pg_1446@tree2921.json
pg_2039@tree4198.json
pg_2042@tree4202.json
pg_1942@tree3962.json
pg_1868@tree3767.json
pg_1567@tree3137.json
pg_244@tree3855.json
pg_2879@tree6674.json
pg_412@tree2166.json
pg_225@tree5991.json
pg_1867@tree3766.json
pg_1278@tree2572.json
pg_1268@tree2560.json
pg_787@tree1489.json
pg_2046@tree5928.json
ot_859@tree1.json
ot_502@tree1.json
ot_764@tree1.json
ot_119@tree1.json
ot_118@tree1.json
ot_425@tree1.json
pg_2577@tree5980.json
ot_731@tree2.json
pg_2866@tree6656.json
pg_2860@tree6646.json
ot_533@tree2.json
ot_773@tree1.json
ot_116@tree1.json
ot_655@tree1.json
ot_121@tree7.json
pg_2876@tree6670.json
pg_2926@tree6757.json
pg_1764@tree6299.json
ot_137@tree1.json
ot_140@tree1.json
ot_806@tree2.json
pg_2798@tree6497.json
ot_104@tree1.json
ot_142@tree1.json
ot_138@tree1.json
pg_2864@tree6651.json
ot_139@tree1.json
ot_415@tree2.json
pg_1872@tree3780.json
ot_125@tree1.json
pg_2869@tree6661.json
ot_112@tree1.json
pg_2853@tree6624.json
ot_123@tree1.json
pg_2872@tree6665.json
ot_122@tree1.json
ot_124@tree1.json
ot_129@tree1.json
ot_147@tree1.json
ot_148@tree1.json
ot_149@tree4.json
ot_504@tree3.json
ot_150@tree3.json
ot_156@tree1.json
ot_153@tree1.json
ot_151@tree1.json
ot_154@tree1.json
ot_155@tree1.json
ot_152@tree1.json
ot_157@tree1.json
ot_158@tree1.json
ot_159@tree1.json
ot_289@tree1.json
ot_144@tree1.json
ot_136@tree1.json
ot_812@tree4.json
ot_305@tree1.json
pg_2857@tree6628.json
pg_1887@tree6629.json
pg_2850@tree6620.json
pg_2444@tree6526.json
pg_2870@tree6662.json
pg_2871@tree6663.json
ot_769@tree3.json
ot_312@tree1.json
ot_166@tree1.json
ot_161@tree1.json
ot_160@tree1.json
pg_1979@tree6300.json
pg_2805@tree6512.json
ot_162@tree1.json
ot_164@tree1.json
ot_313@tree2.json
ot_165@tree1.json
ot_167@tree1.json
pg_2829@tree6579.json
ot_768@tree1.json
ot_170@tree1.json

NO TREE (empty after cleaning)

ot_102@tree1.json
ot_174@tree1.json
ot_110@tree1.json
pg_2845@tree6606.json
ot_172@tree1.json
pg_2454@tree5247.json
pg_2924@tree6755.json
ot_172@tree2.json
ot_173@tree1.json
pg_2600@tree6022.json
ot_176@tree1.json
ot_177@tree1.json
ot_178@tree1.json
pg_2591@tree6024.json
pg_2599@tree6021.json
pg_1966@tree4019.json
pg_2875@tree6668.json
pg_2707@tree6281.json
ot_863@tree2.json
ot_749@tree1.json
ot_770@tree1.json
pg_2404@tree5068.json
pg_1854@tree3743.json
pg_1953@tree3977.json
pg_2890@tree6701.json
ot_103@tree4.json
pg_1586@tree3208.json
pg_2332@tree4912.json
pg_2796@tree6491.json
pg_2692@tree6245.json
ot_101@tree1.json
pg_2858@tree6642.json
ot_171@tree1.json
ot_747@tree3.json
ot_500@tree1.json
pg_420@tree522.json
ot_314@tree1.json
pg_2861@tree6647.json
pg_2859@tree6643.json
pg_1797@tree3635.json
pg_2844@tree6605.json
pg_2843@tree6604.json
pg_2825@tree6572.json
pg_2695@tree6250.json
pg_2656@tree6185.json
pg_1600@tree3231.json
pg_2688@tree6240.json
pg_2359@tree4962.json
pg_2687@tree6239.json
pg_2691@tree6244.json
pg_2685@tree6235.json
ot_168@tree1.json
ot_254@Tr87680.json
pg_1634@tree3303.json
pg_1927@tree6215.json
pg_2587@tree5998.json
pg_1981@tree4052.json
pg_2684@tree6644.json
pg_1428@tree2855.json
pg_1646@tree6231.json
pg_2833@tree6588.json
pg_2834@tree6589.json
pg_2816@tree6556.json
pg_2741@tree6645.json
pg_2589@tree6001.json
pg_2655@tree6181.json
pg_1997@tree6183.json
pg_2654@tree6179.json
pg_2585@tree5994.json
pg_2653@tree6178.json
pg_2657@tree6191.json
pg_2551@tree6180.json
pg_2576@tree5975.json
pg_1870@tree3769.json
ot_979@tree1.json
pg_2659@tree6195.json
ot_181@tree2.json
ot_750@tree2.json
ot_814@tree2.json
pg_2881@tree6680.json
pg_2143@tree4505.json
pg_2098@tree6487.json
pg_2851@tree6621.json
pg_2415@tree5096.json
pg_423@tree2857.json
pg_2573@tree5959.json
pg_2711@tree6295.json
ot_307@tree1.json
pg_2460@tree5285.json
pg_1252@tree2661.json
pg_1336@tree2660.json
pg_1948@tree6513.json
pg_1796@tree6514.json
pg_2243@tree6515.json
pg_2670@tree6214.json
pg_2671@tree6216.json
pg_2673@tree6219.json
pg_2674@tree6220.json
pg_2675@tree6221.json
pg_2676@tree6222.json
pg_2677@tree6223.json
pg_2682@tree6227.json
pg_2683@tree6228.json
pg_2807@tree6519.json
pg_2808@tree6522.json
pg_2667@tree6211.json
pg_2838@tree6594.json
pg_2087@tree4323.json
pg_1988@tree4074.json
pg_2593@tree6247.json
pg_2614@tree6121.json
pg_2628@tree6143.json
pg_2323@tree6537.json
pg_1940@tree3943.json
pg_437@tree6242.json
pg_2594@tree6014.json
pg_2357@tree6538.json
ot_1000@tree1.json
pg_251@tree134.json
pg_1849@tree3731.json
pg_2811@tree6533.json
pg_2604@tree6043.json
pg_1563@tree6170.json
pg_2664@tree6201.json
pg_1776@tree3581.json
ot_185@tree1.json
pg_1337@tree6167.json
pg_2629@tree6162.json
pg_2156@tree5953.json
pg_1338@tree2666.json
pg_2422@tree5117.json
ot_182@tree1.json
ot_183@tree2.json
pg_2061@tree4245.json
pg_2068@tree6488.json
pg_2405@tree6669.json
ot_650@tree1.json
pg_1366@tree6166.json
pg_2092@tree4335.json
pg_2544@tree6482.json
pg_2696@tree6249.json
pg_2709@tree6290.json
pg_2708@tree6289.json
pg_1343@tree6255.json
pg_2678@tree6224.json
pg_421@tree523.json
pg_2710@tree6291.json
pg_1340@tree2669.json
ot_709@tree1.json
ot_659@tree1.json
ot_642@tree1.json
ot_736@tree1.json
ot_505@tree1.json
ot_741@tree1.json
ot_722@tree1.json
ot_805@tree1.json
ot_811@tree1.json
ot_508@tree2.json
ot_509@tree1.json
ot_649@tree1.json
ot_111@tree1.json
pg_335@tree360.json
pg_338@tree5527.json
pg_339@tree365.json
pg_343@tree5534.json
pg_348@tree381.json
pg_349@tree5539.json
pg_353@tree5542.json
pg_358@tree406.json
pg_366@tree5552.json
pg_367@tree418.json
pg_368@tree5553.json
pg_369@tree5554.json
pg_370@tree426.json
pg_372@tree431.json
pg_373@tree432.json
pg_374@tree433.json
pg_375@tree436.json
pg_376@tree438.json
pg_380@tree5560.json
pg_382@tree449.json
pg_387@tree5562.json
pg_389@tree470.json
pg_393@tree482.json
pg_397@tree494.json
pg_399@tree5565.json
pg_400@tree497.json
pg_402@tree5570.json
pg_403@tree503.json
pg_405@tree507.json
pg_407@tree513.json
pg_408@tree5571.json
pg_411@tree518.json
pg_414@tree519.json
pg_430@tree541.json
pg_441@tree5575.json
pg_444@tree564.json
pg_446@tree565.json
pg_447@tree5576.json
pg_448@tree5577.json
pg_449@tree570.json
pg_450@tree574.json
pg_470@tree615.json
pg_471@tree617.json
pg_473@tree623.json
pg_474@tree627.json
pg_475@tree5594.json
pg_477@tree633.json
pg_479@tree636.json
pg_480@tree637.json
pg_481@tree644.json
pg_482@tree5595.json
pg_483@tree647.json
ot_701@Tr90392.json
ot_703@Tr88391.json
ot_705@Tr93612.json
ot_466@Tr89358.json
ot_997@tree1.json
pg_2448@tree5223.json
pg_2739@tree6601.json
pg_2554@tree5580.json
pg_2715@tree6308.json
pg_2753@tree6360.json
pg_263@tree149.json
pg_2542@tree5590.json
pg_2737@tree6322.json
pg_2738@tree6323.json
pg_2738@tree6324.json
pg_2892@tree6700.json
pg_2891@tree6699.json
ot_106@tree1.json
pg_2731@tree6428.json
pg_2713@tree6309.json
pg_2742@tree6342.json
pg_2757@tree6369.json
pg_2553@tree5579.json
pg_2556@tree5586.json
pg_312@tree264.json
pg_313@tree6681.json
pg_2484@tree6607.json
pg_2849@tree6615.json
pg_2822@tree6569.json
ot_892@tree1.json
ot_290@tree1.json
ot_624@tree2.json
ot_711@tree1.json
ot_44@Tr64893.json
ot_19@Tr63070.json

NO TREE (empty after cleaning)

pg_108@tree4130.json
pg_422@tree530.json
ot_278@tree1.json
ot_97@tree4.json
ot_488@Tr77496.json
pg_2404@tree6388.json
ot_623@tree2.json
ot_597@Tr53543.json
pg_2071@tree4264.json
ot_530@Tr81397.json
ot_331@Tr77751.json
ot_340@Tr52077.json
pg_2647@tree6169.json
ot_453@Tr87992.json
pg_1879@tree3796.json
pg_2618@tree6130.json
ot_389@Tr63300.json
ot_115@tree1.json
pg_827@tree1585.json
ot_26@Tr3688.json
pg_2916@tree6744.json
ot_317@Tr53059.json
ot_458@Tr80994.json
pg_2927@tree6760.json
ot_443@Tr74361.json
pg_404@tree505.json
pg_2812@tree6545.json
ot_131@tree1.json
ot_657@tree4.json
ot_535@tree1.json
ot_534@tree1.json
ot_546@Tr85942.json
ot_105@tree1.json
ot_114@tree1.json
ot_132@tree1.json
ot_218@tree4.json
ot_221@Tr72273.json
ot_26@Tr3687.json
ot_435@Tr70597.json
ot_445@Tr75519.json
pg_1879@tree3798.json
ot_447@Tr75532.json
ot_555@Tr92138.json
ot_559@Tr70451.json
ot_647@tree2.json
pg_580@tree856.json
pg_1217@tree2455.json
pg_1632@tree3298.json
pg_2701@tree6271.json
pg_2775@tree6432.json
pg_2793@tree6705.json
pg_2813@tree6550.json
pg_2874@tree6667.json
pg_2889@tree6698.json
pg_2814@tree6551.json
ot_752@tree1.json
ot_306@tree1.json