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evoinfo / miapa

Minimum Information About a Phylogenetic Analysis (MIAPA) vocabularies and tools
http://www.evoio.org/wiki/MIAPA
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treatment of gap characters #28

Closed rossmounce closed 7 years ago

rossmounce commented 7 years ago

The matrix itself may well contain gap characters after alignment. The analysis isn't reproducible if you don't know how these gaps were treated in the tree inference stage, and the effects between different treatments can often be non-trivial. The treatment can't be inferred simply from looking at the matrix or software used in most cases.

If it's judged not "important enough" then fine. But I thought I'd propose it here anyhow.

Has it been been discussed for inclusion before? Apologies if it has.

hlapp commented 7 years ago

@kcranston @mtholder @arlin any comments? I'd go ahead and merge otherwise.

mtholder commented 7 years ago

:+1: certainly need to know how gaps are handled if you wanted to understand an analysis.

kcranston commented 7 years ago

+1 from me as well

hlapp commented 7 years ago

Thanks @rossmounce !