Analysis Description
--------------------
MEME (Mixed Effects Model of Evolution) estimates a site-wise synonymous
(α) and a two-category mixture of non-synonymous (β-, with
proportion p-, and β+ with proportion [1-p-]) rates, and uses a
likelihood ratio test to determine if β+ > α at a site. The
estimates aggregate information over a proportion of branches at a site,
so the signal is derived from episodic diversification, which is a
combination of strength of selection [effect size] and the proportion of
the tree affected. A subset of branches can be selected for testing as
well, in which case an additional (nuisance) parameter will be inferred
-- the non-synonymous rate on branches NOT selected for testing.
Multiple partitions within a NEXUS file are also supported for
recombination - aware analysis. 

- __Requirements__: in-frame codon alignment and a phylogenetic tree

- __Citation__: Detecting Individual Sites Subject to Episodic Diversifying Selection.
_PLoS Genet_ 8(7): e1002764.

- __Written by__: Sergei L. Kosakovsky Pond, Steven Weaver

- __Contact Information__: spond@temple.edu

- __Analysis Version__: 2.1.1



####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/`) 

>Please select a tree file for the data: (`/home/datamonkey/`) 
>Loaded a multiple sequence alignment with **20** sequences, **845** codons, and **1** partitions from `/home/datamonkey/datamonkey-js-server/production/app/meme/output/5ddcaf843b682c361e77b34e`


####Choose the set of branches to test for selection

1. [**All**] Include all branches in the analysis
2. [**Internal**] Include all internal branches in the analysis
3. [**Leaves**] Include all leaf branches in the analysis
4. [**Unlabeled branches**] Set of 37 unlabeled branches

>Please choose an option (or press q to cancel selection):
>Select the p-value threshold to use when testing for selection (permissible range = [0,1], default value = 0.1): 

>Save the resulting JSON file to (`/home/datamonkey/`) 

### Branches to include in the MEME analysis
Selected 37 branches to include in the MEME analysis: `ATTLR1, PFTLR1, MMTLR1, Node11, Node9, IPTLR1, Node8, CBTLR1, Node7, MATLR1, Node6, ONTLR1, SMTLR1, TFTLR1, Node23, DRTLR1, Node22, LCTLR1, Node21, PHTLR1, Node20, Node18, ECTLR1, Node17, Node5, CITLR1, Node4, OFTLR1, Node3, SATLR1, Node2, CCTLR1, Node1, TOTLR1, LMTLR1, Node34, TRTLR1`


### Obtaining branch lengths and nucleotide substitution biases under the nucleotide GTR model
* Log(L) = -58492.16, AIC-c = 117074.41 (45 estimated parameters)

### Obtaining the global omega estimate based on relative GTR branch lengths and nucleotide substitution biases
* Log(L) = -57399.33, AIC-c = 114902.99 (52 estimated parameters)
* non-synonymous/synonymous rate ratio for *test* =   0.6840

### Improving branch lengths, nucleotide substitution biases, and global dN/dS ratios under a full codon model
* Log(L) = -65457.20
* non-synonymous/synonymous rate ratio for *test* = 10000.0000

### For partition 1 these sites are significant at p <=0.1

|   Codon    | Partition  |   alpha    |   beta+    |     p+     |    LRT     |Episodic selection detected?| # branches |
|:----------:|:----------:|:----------:|:----------:|:----------:|:----------:|:--------------------------:|:----------:|
|     7      |     1      |    0.000   |  3249.371  |    0.422   |   15.908   |      Yes, p =  0.0001      |     1      |
|     8      |     1      |    0.001   |  5963.834  |    0.292   |   13.599   |      Yes, p =  0.0005      |     2      |
|     13     |     1      |    0.136   |  9999.997  |    0.132   |   17.385   |      Yes, p =  0.0001      |     1      |
|     15     |     1      |    0.001   |10000.000...|    0.341   |   19.106   |      Yes, p =  0.0000      |     1      |
|     20     |     1      |    0.565   |  1843.061  |    0.150   |   16.759   |      Yes, p =  0.0001      |     1      |
|     22     |     1      |    0.000   |  4114.538  |    0.251   |   69.247   |      Yes, p =  0.0000      |     2      |
|     26     |     1      |    0.158   |  7649.062  |    0.256   |    7.115   |      Yes, p =  0.0127      |     0      |
|     28     |     1      |    0.065   |  2380.870  |    0.151   |   19.249   |      Yes, p =  0.0000      |     1      |