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/61eec4295e56f71949c04edd.FADE.cache
> FADE will write cache and result files to _/home/datamonkey/datamonkey-js-server/production/app/fade/output/61eec4295e56f71949c04edd.FADE.cache_ and _/home/datamonkey/datamonkey-js-server/production/app/fade/output/61eec4295e56f71949c04edd.FADE.json_, respectively 




### Loaded **59** sequences, **3231** sites, and **1** partitions from `/home/datamonkey/datamonkey-js-server/production/app/fade/output/61eec4295e56f71949c04edd`
Error:
Input tree MUST be rooted in call to assert(((fade.partitions_and_trees[index])[terms.data.tree])[terms.trees.rooted], "Input tree MUST be rooted");

Function call stack
1 :  assert(((fade.partitions_and_trees[index])[terms.data.tree])[terms.trees.rooted], "Input tree MUST be rooted");

	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/61eec4295e56f71949c04edd.tre"
		}
-------