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>Select a coding sequence alignment file (`/Users/chasenelson/Documents/GitHub/evogenomics_hyphy/datasets/`) ksr2.fna
>Loaded a multiple sequence alignment with **9** sequences, **949** codons, and **1** partitions from `/Users/chasenelson/Documents/GitHub/evogenomics_hyphy/datasets/ksr2.fna`

>branches => All

>srv => Yes
The number omega rate classes to include in the model (permissible range = [1,10], default value = 3, integer): 
>rates => 3

>multiple-hits => None
The number alpha rate classes to include in the model [1-10, default 3] (permissible range = [1,10], default value = 3, integer): 
>syn-rates => 3

>error-sink => No
The number of points in the initial distributional guess for likelihood fitting (permissible range = [1,10000], default value = 250, integer): 
>grid-size => 250
The number of initial random guesses to 'seed' rate values optimization (permissible range = [1,25], default value = 1, integer): 
>starting-points => 1


### Branches to test for selection in the BUSTED analysis
* Selected 15 branches to test in the BUSTED analysis: `HUM, PAN, Node6, GOR, Node5, PON, Node4, GIB, Node3, MAC, BAB, Node12, Node2, MAR, BUS`


### Obtaining branch lengths and nucleotide substitution biases under the nucleotide GTR model

>kill-zero-lengths => Yes
* Log(L) = -5768.11, AIC-c = 11582.26 (23 estimated parameters)
* 1 partition. Total tree length by partition (subs/site)  0.121

### Obtaining the global omega estimate based on relative GTR branch lengths and nucleotide substitution biases
* Log(L) = -5342.82, AIC-c = 10745.85 (30 estimated parameters)
* 1 partition. Total tree length by partition (subs/site)  0.134
* non-synonymous/synonymous rate ratio for *test* =   0.0341

### Improving branch lengths, nucleotide substitution biases, and global dN/dS ratios under a full codon model
* Log(L) = -5333.75, AIC-c = 10727.71 (30 estimated parameters)
* non-synonymous/synonymous rate ratio for *test* =   0.0306

### Performing the full (dN/dS > 1 allowed) branch-site model fit
* Log(L) = -5300.23, AIC-c = 10678.82 (39 estimated parameters)
* For *test* branches, the following rate distribution for branch-site combinations was inferred

|          Selection mode           |     dN/dS     |Proportion, %|               Notes               |
|-----------------------------------|---------------|-------------|-----------------------------------|
|        Negative selection         |     0.000     |    5.581    |                                   |
|        Negative selection         |     0.012     |   94.046    |                                   |
|      Diversifying selection       |     9.781     |    0.374    |                                   |

* The following rate distribution for site-to-site **synonymous** rate variation was inferred

|               Rate                | Proportion, % |               Notes               |
|-----------------------------------|---------------|-----------------------------------|
|               0.398               |    32.899     |                                   |
|               0.420               |    52.826     |                                   |
|               4.533               |    14.275     |                                   |


### Performing the constrained (dN/dS > 1 not allowed) model fit
* Log(L) = -5301.39, AIC-c = 10679.13 (38 estimated parameters)
* For *test* branches under the null (no dN/dS > 1 model), the following rate distribution for branch-site combinations was inferred

|          Selection mode           |     dN/dS     |Proportion, %|               Notes               |
|-----------------------------------|---------------|-------------|-----------------------------------|
|        Negative selection         |     0.000     |   89.934    |                                   |
|        Negative selection         |     0.000     |    6.759    |       Collapsed rate class        |
|         Neutral evolution         |     1.000     |    3.307    |                                   |

* The following rate distribution for site-to-site **synonymous** rate variation was inferred

|               Rate                | Proportion, % |               Notes               |
|-----------------------------------|---------------|-----------------------------------|
|               0.381               |    85.219     |                                   |
|               3.603               |    13.886     |                                   |
|              19.555               |     0.895     |                                   |

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## Branch-site unrestricted statistical test of episodic diversification [BUSTED]
Likelihood ratio test for episodic diversifying positive selection, **p =   0.1564**.