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@rdmpage
Created March 25, 2015 10:55
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BOLD phylogeny from API
BOLD has a (hidden) API to retrieve a Newick tree for a BIN. For example on the page http://www.boldsystems.org/index.php/Public_BarcodeCluster?clusteruri=BOLD:AAD8242 we see an SVG tree. Under the hood this is called by: http://www.boldsystems.org/index.php/Public_Ajax_BINTree?clusterguid=BOLD:AAD8242&clusteruri=BOLD:AAD8242&clustername=BIN38242&clusterid=1738567
It's not clear where the "clusterid" comes from, but without it the API call fails.
{"treeNewick":"(B. monticola:0.00000,((((((((((((((((B. monticola:0.00000,(B. monticola:0.00000,(B. monticola:0.00000,(((((((B. monticola:-0.00000,B. monticola:0.00000):0.00000,B. monticola:0.00000):0.00000,B. monticola:0.00000):0.00000,B. monticola:0.00000):0.00000,B. monticola:0.00000):0.00000,B. monticola:0.00000):0.00000,B. monticola:0.00000):0.00000):0.00000):0.00000):0.00000,(B. monticola:0.00000,B. monticola:-0.00000):0.00150):0.00000,B. monticola:0.00000):0.00069,((((B. monticola:0.00000,B. monticola:-0.00000):0.00000,(B. monticola:0.00000,B. monticola:-0.00000):0.00000):0.00003,Bombus:0.00147):0.00004,B. monticola:0.00151):0.00144):0.00009,B. monticola:0.00000):0.00000,B. monticola:0.00000):0.00000,B. monticola:0.00000):0.00032,((B. monticola:0.00000,B. monticola:-0.00000):0.00000,B. monticola:0.00000):0.00044):0.00000,B. monticola:0.00000):0.00076,B. monticola:0.00000):0.00000,B. monticola:0.00000):0.00000,B. monticola:0.00000):0.00000,B. monticola:0.00000):0.00000,B. monticola:0.00000):0.00000,B. monticola:0.00000):0.00000,B. monticola:0.00000):0.00000,(((((((((((((((Nearest BIN -outgroup-nn**:0.01276,(((((B. sylvicola:0.00000,B. sylvicola:-0.00000):0.00640,B. monticola:0.00285):0.00000,B. monticola:0.00000):0.00155,B. monticola:0.00000):0.00180,B. monticola:0.00204):0.00340):0.00000,B. monticola:0.00000):0.00364,B. monticola:0.00000):0.00555,B. monticola:0.00193):0.00125,B. monticola:0.00010):0.00147,((B. monticola:-0.00000,B. monticola:0.00000):0.00000,B. monticola:0.00000):0.00084):0.00065,(B. monticola:0.00000,(B. monticola:0.00000,B. monticola:-0.00000):0.00000):0.00101):0.00006,B. monticola:0.00000):0.00000,B. monticola:0.00000):0.00000,B. monticola:0.00000):0.00000,B. monticola:0.00000):0.00000,B. monticola:0.00000):0.00000,B. monticola:0.00000):0.00000,B. monticola:0.00000):0.00000,(B. monticola:0.00000,(B. monticola:0.00000,(B. monticola:0.00000,(B. monticola:0.00000,(B. monticola:0.00000,(B. monticola:0.00000,(B. monticola:0.00000,(B. monticola:0.00150,B. monticola:0.00000):0.00000):0.00000):0.00000):0.00000):0.00000):0.00000):0.00000):0.00000):0.00000);","treePdf":"http:\/\/131.104.63.51\/results\/jobs\/barcode.phyloTree_barcode_525EBD05-7E72-483E-A36A-7FA193FD7351.H:bold_jobserver-vm:842584\/finaltree.pdf"}
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