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 15 nonempty trees after cleaning. The files of interest in this directory are:

JSON log of pruningpruned newick
ot_733@tree2.json
ot_735@tree1.json
ot_737@tree1.json
ot_738@tree1.json

NO TREE (empty after cleaning)

ot_739@tree1.json
ot_764@tree1.json

NO TREE (empty after cleaning)

ot_119@tree1.json

NO TREE (empty after cleaning)

ot_118@tree1.json

NO TREE (empty after cleaning)

pg_2577@tree5980.json

NO TREE (empty after cleaning)

pg_2866@tree6656.json

NO TREE (empty after cleaning)

pg_2860@tree6646.json

NO TREE (empty after cleaning)

ot_116@tree1.json

NO TREE (empty after cleaning)

ot_121@tree7.json

NO TREE (empty after cleaning)

pg_2876@tree6670.json

NO TREE (empty after cleaning)

pg_2926@tree6757.json

NO TREE (empty after cleaning)

pg_1764@tree6299.json

NO TREE (empty after cleaning)

ot_137@tree1.json

NO TREE (empty after cleaning)

ot_140@tree1.json

NO TREE (empty after cleaning)

pg_2798@tree6497.json

NO TREE (empty after cleaning)

ot_104@tree1.json

NO TREE (empty after cleaning)

ot_142@tree1.json

NO TREE (empty after cleaning)

ot_138@tree1.json

NO TREE (empty after cleaning)

pg_2864@tree6651.json

NO TREE (empty after cleaning)

ot_139@tree1.json

NO TREE (empty after cleaning)

pg_1872@tree3780.json

NO TREE (empty after cleaning)

ot_125@tree1.json

NO TREE (empty after cleaning)

pg_2869@tree6661.json

NO TREE (empty after cleaning)

ot_112@tree1.json

NO TREE (empty after cleaning)

pg_2853@tree6624.json

NO TREE (empty after cleaning)

ot_123@tree1.json

NO TREE (empty after cleaning)

pg_2872@tree6665.json

NO TREE (empty after cleaning)

ot_122@tree1.json

NO TREE (empty after cleaning)

ot_124@tree1.json

NO TREE (empty after cleaning)

ot_129@tree1.json

NO TREE (empty after cleaning)

ot_147@tree1.json

NO TREE (empty after cleaning)

ot_148@tree1.json

NO TREE (empty after cleaning)

ot_149@tree4.json

NO TREE (empty after cleaning)

ot_150@tree3.json

NO TREE (empty after cleaning)

ot_156@tree1.json

NO TREE (empty after cleaning)

ot_153@tree1.json

NO TREE (empty after cleaning)

ot_151@tree1.json

NO TREE (empty after cleaning)

ot_154@tree1.json

NO TREE (empty after cleaning)

ot_155@tree1.json

NO TREE (empty after cleaning)

ot_152@tree1.json

NO TREE (empty after cleaning)

ot_157@tree1.json

NO TREE (empty after cleaning)

ot_158@tree1.json

NO TREE (empty after cleaning)

ot_159@tree1.json

NO TREE (empty after cleaning)

ot_144@tree1.json

NO TREE (empty after cleaning)

ot_136@tree1.json

NO TREE (empty after cleaning)

pg_2857@tree6628.json

NO TREE (empty after cleaning)

pg_1887@tree6629.json

NO TREE (empty after cleaning)

pg_2850@tree6620.json

NO TREE (empty after cleaning)

pg_2444@tree6526.json

NO TREE (empty after cleaning)

pg_2870@tree6662.json

NO TREE (empty after cleaning)

pg_2871@tree6663.json

NO TREE (empty after cleaning)

ot_166@tree1.json

NO TREE (empty after cleaning)

ot_161@tree1.json

NO TREE (empty after cleaning)

ot_160@tree1.json

NO TREE (empty after cleaning)

pg_1979@tree6300.json

NO TREE (empty after cleaning)

pg_2805@tree6512.json

NO TREE (empty after cleaning)

ot_162@tree1.json

NO TREE (empty after cleaning)

ot_164@tree1.json

NO TREE (empty after cleaning)

ot_165@tree1.json

NO TREE (empty after cleaning)

ot_167@tree1.json

NO TREE (empty after cleaning)

ot_170@tree1.json

NO TREE (empty after cleaning)

ot_102@tree1.json

NO TREE (empty after cleaning)

ot_174@tree1.json

NO TREE (empty after cleaning)

ot_110@tree1.json

NO TREE (empty after cleaning)

pg_2845@tree6606.json

NO TREE (empty after cleaning)

ot_172@tree1.json

NO TREE (empty after cleaning)

pg_2454@tree5247.json

NO TREE (empty after cleaning)

ot_172@tree2.json

NO TREE (empty after cleaning)

ot_173@tree1.json

NO TREE (empty after cleaning)

pg_2600@tree6022.json

NO TREE (empty after cleaning)

ot_176@tree1.json

NO TREE (empty after cleaning)

ot_177@tree1.json

NO TREE (empty after cleaning)

ot_178@tree1.json

NO TREE (empty after cleaning)

pg_2591@tree6024.json

NO TREE (empty after cleaning)

pg_2599@tree6021.json

NO TREE (empty after cleaning)

pg_1966@tree4019.json

NO TREE (empty after cleaning)

pg_2875@tree6668.json

NO TREE (empty after cleaning)

pg_2707@tree6281.json

NO TREE (empty after cleaning)

pg_2404@tree5068.json

NO TREE (empty after cleaning)

pg_420@tree522.json

NO TREE (empty after cleaning)

pg_2861@tree6647.json

NO TREE (empty after cleaning)

pg_2859@tree6643.json

NO TREE (empty after cleaning)

pg_1797@tree3635.json

NO TREE (empty after cleaning)

pg_2844@tree6605.json

NO TREE (empty after cleaning)

pg_2843@tree6604.json

NO TREE (empty after cleaning)

pg_2825@tree6572.json

NO TREE (empty after cleaning)

pg_2695@tree6250.json

NO TREE (empty after cleaning)

pg_2656@tree6185.json

NO TREE (empty after cleaning)

pg_1600@tree3231.json

NO TREE (empty after cleaning)

pg_2688@tree6240.json

NO TREE (empty after cleaning)

pg_2359@tree4962.json

NO TREE (empty after cleaning)

pg_2687@tree6239.json

NO TREE (empty after cleaning)

pg_2691@tree6244.json

NO TREE (empty after cleaning)

pg_2685@tree6235.json

NO TREE (empty after cleaning)

ot_168@tree1.json

NO TREE (empty after cleaning)

pg_1634@tree3303.json

NO TREE (empty after cleaning)

pg_1927@tree6215.json

NO TREE (empty after cleaning)

pg_2587@tree5998.json

NO TREE (empty after cleaning)

pg_1981@tree4052.json

NO TREE (empty after cleaning)

pg_2684@tree6644.json

NO TREE (empty after cleaning)

pg_1428@tree2855.json

NO TREE (empty after cleaning)

pg_1646@tree6231.json

NO TREE (empty after cleaning)

pg_2833@tree6588.json

NO TREE (empty after cleaning)

pg_2834@tree6589.json

NO TREE (empty after cleaning)

pg_2816@tree6556.json

NO TREE (empty after cleaning)

pg_2741@tree6645.json

NO TREE (empty after cleaning)

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
pg_2659@tree6195.json
ot_181@tree2.json

NO TREE (empty after cleaning)

pg_2881@tree6680.json

NO TREE (empty after cleaning)

pg_2143@tree4505.json

NO TREE (empty after cleaning)

pg_2098@tree6487.json

NO TREE (empty after cleaning)

pg_2851@tree6621.json

NO TREE (empty after cleaning)

pg_2415@tree5096.json

NO TREE (empty after cleaning)

pg_423@tree2857.json

NO TREE (empty after cleaning)

pg_2573@tree5959.json

NO TREE (empty after cleaning)

pg_2711@tree6295.json

NO TREE (empty after cleaning)

pg_2460@tree5285.json

NO TREE (empty after cleaning)

pg_1252@tree2661.json

NO TREE (empty after cleaning)

pg_1336@tree2660.json

NO TREE (empty after cleaning)

pg_1948@tree6513.json

NO TREE (empty after cleaning)

pg_1796@tree6514.json

NO TREE (empty after cleaning)

pg_2243@tree6515.json

NO TREE (empty after cleaning)

pg_2670@tree6214.json

NO TREE (empty after cleaning)

pg_2671@tree6216.json

NO TREE (empty after cleaning)

pg_2673@tree6219.json

NO TREE (empty after cleaning)

pg_2674@tree6220.json

NO TREE (empty after cleaning)

pg_2675@tree6221.json

NO TREE (empty after cleaning)

pg_2676@tree6222.json

NO TREE (empty after cleaning)

pg_2677@tree6223.json

NO TREE (empty after cleaning)

pg_2682@tree6227.json

NO TREE (empty after cleaning)

pg_2683@tree6228.json

NO TREE (empty after cleaning)

pg_2807@tree6519.json

NO TREE (empty after cleaning)

pg_2808@tree6522.json

NO TREE (empty after cleaning)

pg_2667@tree6211.json

NO TREE (empty after cleaning)

pg_2838@tree6594.json

NO TREE (empty after cleaning)

pg_2087@tree4323.json

NO TREE (empty after cleaning)

pg_1988@tree4074.json

NO TREE (empty after cleaning)

pg_2593@tree6247.json

NO TREE (empty after cleaning)

pg_2614@tree6121.json

NO TREE (empty after cleaning)

pg_2628@tree6143.json

NO TREE (empty after cleaning)

pg_2323@tree6537.json

NO TREE (empty after cleaning)

pg_1940@tree3943.json

NO TREE (empty after cleaning)

pg_437@tree6242.json

NO TREE (empty after cleaning)

pg_2594@tree6014.json

NO TREE (empty after cleaning)

pg_2357@tree6538.json

NO TREE (empty after cleaning)

pg_251@tree134.json

NO TREE (empty after cleaning)

pg_1849@tree3731.json

NO TREE (empty after cleaning)

pg_2811@tree6533.json

NO TREE (empty after cleaning)

pg_2604@tree6043.json

NO TREE (empty after cleaning)

pg_1563@tree6170.json

NO TREE (empty after cleaning)

pg_2664@tree6201.json

NO TREE (empty after cleaning)

pg_1776@tree3581.json

NO TREE (empty after cleaning)

ot_185@tree1.json

NO TREE (empty after cleaning)

pg_1337@tree6167.json

NO TREE (empty after cleaning)

pg_2629@tree6162.json

NO TREE (empty after cleaning)

pg_2156@tree5953.json

NO TREE (empty after cleaning)

pg_1338@tree2666.json

NO TREE (empty after cleaning)

pg_2422@tree5117.json

NO TREE (empty after cleaning)

ot_182@tree1.json

NO TREE (empty after cleaning)

ot_183@tree2.json

NO TREE (empty after cleaning)

pg_2061@tree4245.json

NO TREE (empty after cleaning)

pg_2068@tree6488.json

NO TREE (empty after cleaning)

pg_2405@tree6669.json

NO TREE (empty after cleaning)

pg_1366@tree6166.json

NO TREE (empty after cleaning)

pg_2092@tree4335.json

NO TREE (empty after cleaning)

pg_2544@tree6482.json

NO TREE (empty after cleaning)

pg_2696@tree6249.json

NO TREE (empty after cleaning)

pg_2709@tree6290.json

NO TREE (empty after cleaning)

pg_2842@tree6603.json

NO TREE (empty after cleaning)

pg_2708@tree6289.json

NO TREE (empty after cleaning)

pg_1343@tree6255.json

NO TREE (empty after cleaning)

pg_1788@tree6534.json

NO TREE (empty after cleaning)

pg_1786@tree6257.json

NO TREE (empty after cleaning)

pg_2678@tree6224.json

NO TREE (empty after cleaning)

pg_421@tree523.json

NO TREE (empty after cleaning)

pg_1761@tree6151.json

NO TREE (empty after cleaning)

pg_2710@tree6291.json

NO TREE (empty after cleaning)

pg_1340@tree2669.json

NO TREE (empty after cleaning)

ot_709@tree1.json

NO TREE (empty after cleaning)

ot_659@tree1.json

NO TREE (empty after cleaning)

ot_642@tree1.json

NO TREE (empty after cleaning)

ot_736@tree1.json

NO TREE (empty after cleaning)

ot_505@tree1.json

NO TREE (empty after cleaning)

ot_741@tree1.json

NO TREE (empty after cleaning)

ot_722@tree1.json

NO TREE (empty after cleaning)