Analysis Description
--------------------
FADE (FUBAR Approach to Directional Evolution) is a fast method to test
whether or not a subset of sites in a protein alignment evolve towards a
particular residue along a subset of branches at accelerated rates
compared to reference model. FADE uses a random effects model and latent
Dirichlet allocation (LDA) - inspired approximation methods to allocate
sites to rate classes.

- __Requirements__: A protein alignment and a **rooted** phylogenetic tree (optionally
annotated with {})

- __Citation__: TBD

- __Written by__: Sergei L Kosakovsky Pond

- __Contact Information__: spond@temple.edu

- __Analysis Version__: 0.2

Save FADE cache to : 
>cache –> /home/datamonkey/datamonkey-js-server/production/app/fade/output/61eec30b5e56f71949c04e96.FADE.cache
> FADE will write cache and result files to _/home/datamonkey/datamonkey-js-server/production/app/fade/output/61eec30b5e56f71949c04e96.FADE.cache_ and _/home/datamonkey/datamonkey-js-server/production/app/fade/output/61eec30b5e56f71949c04e96.FADE.json_, respectively 


Error:
Can't create empty trees.

Function call stack
1 :  [namespace = aZVsfEol] Topology T = (tree_string);

	Keyword arguments:
		{
		 "branches":"All",
		 "burn-in":"1000000",
		 "chain":"5",
		 "chains":"2000000",
		 "concentration_parameter":"0.5",
		 "grid":"20",
		 "method":"Variational-Bayes",
		 "model":"LG",
		 "samples":"100",
		 "tree":"/home/datamonkey/datamonkey-js-server/production/app/fade/output/61eec30b5e56f71949c04e96.tre"
		}
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2 :  [namespace = cYPqFcLK] result=trees.ExtractTreeInfo(trees.GetTreeString(look_for_newick_tree));
-------
3 :  [namespace = Cu_XFtQ_] partrees+{utility.getGlobalValue("terms.data.name"):partitions[i][0],utility.getGlobalValue("terms.data.filter_string"):partitions[i][1],utility.getGlobalValue("terms.data.tree"):trees.LoadAnnotatedTopologyAndMap(tree_matrix[i][1],mapping)};
-------
4 :  fade.partitions_and_trees=trees.LoadAnnotatedTreeTopology.match_partitions(fade.alignment_info[utility.getGlobalValue("terms.data.partitions")],fade.alignment_info[utility.getGlobalValue("terms.data.name_mapping")]);
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