Analysis Description
--------------------
Perform a Fast Unbiased AppRoximate Bayesian (FUBAR) analysis of a
coding sequence alignment to determine whether some sites have been
subject to pervasive purifying or diversifying selection. Please note
that a FUBAR analysis generates a cache and a results JSON file in the
same directory as directory as the original alignment. HyPhy needs to
have write privileges to this directory. For example if the original
file is in /home/sergei/FUBAR/data/pol.nex then at the end of a FUBAR
run, there will also exist FUBAR-generated files
/home/sergei/FUBAR/data/pol.nex.FUBAR.json,
/home/sergei/FUBAR/data/pol.nex.fubrar.cache. They also provide
checkpointing so that a partially completed analysis can be restarted.

- __Requirements__: in-frame codon alignment (possibly partitioned) and a phylogenetic tree
(one per partition)

- __Citation__: FUBAR: a fast, unconstrained bayesian approximation for inferring
selection (2013), Mol Biol Evol. 30(5):1196-205

- __Written by__: Sergei L Kosakovsky Pond

- __Contact Information__: spond@temple.edu

- __Analysis Version__: 2.0



####Choose Genetic Code

1. [**Universal**] Universal code. (Genebank transl_table=1).
2. [**Vertebrate mtDNA**] Vertebrate mitochondrial DNA code. (Genebank transl_table=2).
3. [**Yeast mtDNA**] Yeast mitochondrial DNA code. (Genebank transl_table=3).
4. [**Mold/Protozoan mtDNA**] Mold, Protozoan and Coelenterate mitochondrial DNA and the Mycloplasma/Spiroplasma code. (Genebank transl_table=4).
5. [**Invertebrate mtDNA**] Invertebrate mitochondrial DNA code. (Genebank transl_table=5).
6. [**Ciliate Nuclear**] Ciliate, Dasycladacean and Hexamita Nuclear code. (Genebank transl_table=6).
7. [**Echinoderm mtDNA**] Echinoderm mitochondrial DNA code. (Genebank transl_table=9).
8. [**Euplotid Nuclear**] Euplotid Nuclear code. (Genebank transl_table=10).
9. [**Alt. Yeast Nuclear**] Alternative Yeast Nuclear code. (Genebank transl_table=12).
10. [**Ascidian mtDNA**] Ascidian mitochondrial DNA code. (Genebank transl_table=13).
11. [**Flatworm mtDNA**] Flatworm mitochondrial DNA code. (Genebank transl_table=14).
12. [**Blepharisma Nuclear**] Blepharisma Nuclear code. (Genebank transl_table=15).
13. [**Chlorophycean mtDNA**] Chlorophycean Mitochondrial Code (transl_table=16).
14. [**Trematode mtDNA**] Trematode Mitochondrial Code (transl_table=21).
15. [**Scenedesmus obliquus mtDNA**] Scenedesmus obliquus mitochondrial Code (transl_table=22).
16. [**Thraustochytrium mtDNA**] Thraustochytrium Mitochondrial Code (transl_table=23).
17. [**Pterobranchia mtDNA**] Pterobranchia Mitochondrial Code (transl_table=24).
18. [**SR1 and Gracilibacteria**] Candidate Division SR1 and Gracilibacteria Code (transl_table=25).
19. [**Pachysolen Nuclear**] Pachysolen tannophilus Nuclear Code (transl_table=26).

>Please choose an option (or press q to cancel selection):

>Select a coding sequence alignment file (`/home/datamonkey/datamonkey-js-test/app/fubar/../../.hyphy/res//TemplateBatchFiles/SelectionAnalyses/`) 

>Please select a tree file for the data: (`/home/datamonkey/datamonkey-js-test/app/fubar/../../.hyphy/res//TemplateBatchFiles/SelectionAnalyses/`) 
>Loaded a multiple sequence alignment with **4** sequences, **2757** codons, and **1** partitions from `/home/datamonkey/datamonkey-js-test/app/fubar/output/5b622feca1e50e1b094766de`
> FUBAR will write cache and result files to _/home/datamonkey/datamonkey-js-test/app/fubar/output/5b622feca1e50e1b094766de.FUBAR.cache_ and _/home/datamonkey/datamonkey-js-test/app/fubar/output/5b622feca1e50e1b094766de.FUBAR.json_, respectively 


> Number of grid points per dimension (total number is D^2) (permissible range = [5,50], default value = 20, integer): > Number of MCMC chains to run (permissible range = [2,20], default value = 5, integer): > The length of each chain (permissible range = [500000,50000000], default value = 2000000, integer): > Use this many samples as burn-in (permissible range = [100000,1900000], default value = 1000000, integer): > How many samples should be drawn from each chain (permissible range = [50,1000000], default value = 100, integer): > The concentration parameter of the Dirichlet prior (permissible range = [0.001,1], default value = 0.5): 

### Obtaining branch lengths and nucleotide substitution biases under the nucleotide GTR model
* Log(L) = -22832.62, AIC-c = 45691.26 (13 estimated parameters)
* Tree length (expected substitutions/site) for partition 1 :    0.459

### Computing the phylogenetic likelihood function on the grid 
* Determining appropriate tree scaling based on the best score from a  20 x 20 rate grid
* Best scaling achieved for 
	* synonymous rate =  7.125
	* non-synonymous rate =  0.214
* Computing conditional site likelihoods on a 20 x 20 rate grid

### Running MCMC chains to obtain a posterior sample of (synonymous,non-synonymous) rate weights
* Using the following settings
	* Number of chains : 5
	* Steps/chain      : 2000000
	* Burn-in steps    : 1000000
	* Samples/chain    : 100
	* Dirichlet alpha  : 0.5
* Running MCMC chain 1
* Running MCMC chain 2
* Running MCMC chain 3
* Running MCMC chain 4
* Running MCMC chain 5