Updating Datamonkey to support new analysis options in HyPhy.

[spond]

Note

This issue exists to track and prioritize updating Datamonkey options and viz to support what is available in HyPhy for key analyses. Keeping the issue open as it will evolve.

FEL

• Enable Datamonkey support for multiple hits (@stevenweaver)

Two CLI flags need to be supported

--multiple-hits

1. [Double] Include branch-specific rates for double nucleotide substitutions
2. [Double+Triple] Include branch-specific rates for double and triple nucleotide substitutions
3. [None] [Default] Use standard models which permit only single nucleotide changes to occur instantly

--site-multihit

This option only makes sense if --multiple-hits is not None.

1. [Estimate][Default] Include branch-specific rates for double nucleotide substitutions
2. [Global] Use a plug-in estimate derived from the global model fit

• Enable FEL Observable viz to support multiple hits (@spond). Presently, multiple hit information is ignored in the viz.

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MEME

• Enable Datamonkey support for multiple hits (@stevenweaver)

Two CLI flags need to be supported

--multiple-hits

1. [Double] Include branch-specific rates for double nucleotide substitutions
2. [Double+Triple] Include branch-specific rates for double and triple nucleotide substitutions
3. [None] [Default] Use standard models which permit only single nucleotide changes to occur instantly

--site-multihit

This option only makes sense if --multiple-hits is not None.

1. [Estimate][Default] Include branch-specific rates for double nucleotide substitutions
2. [Global] Use a plug-in estimate derived from the global model fit

• Enable MEME Observable viz to support multiple hits (@spond). Presently, multiple hit information is ignored in the viz.

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• Enable Datamonkey support for more than two rate categories per site (@stevenweaver)

An additional CLI needs supporting --rates. Valid values are integers 2,3 or 4. The default is 2.

• Enable MEME Observable viz to support multiple hits (@spond). Presently, more than two rate classes will not be correctly supported in the viz.

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• Enable Datamonkey support for more resampling like FEL (@stevenweaver)

Provide support for a CLI --resample (like in FEL, currently). Valid values are non-negative integers, with 0 as the default.

• This is supported by the viz in Observable.

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• Enable Datamonkey support for more character imputation

An additional CLI needs supporting --impute-states. Valid values are Yes or No. The default is No.

• Enable MEME Observable viz to support imputed states (@spond). Presently, imputed states are ignored.