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How is gaps treated in Datamonkey? (Read 3688 times)
Jae
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Curious HyPhy user

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How is gaps treated in Datamonkey?
Oct 8th, 2013 at 3:33pm
 
Hello!

I had a general question of how gaps (ie. "-") are dealt in datamonkey?
I understand on the standalone hyphy there are options to ignore it or not and etc but what about in datamonkey? Does it completely ignore alignment positions with gaps?
I've been using BranchREL and MEME and was wondering if the two methods in datamonkey treats gaps the same way.

I've had numerous help from the developers before and thank you once again!

Jae
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Sergei
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Datamonkeys are forever...

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Re: How is gaps treated in Datamonkey?
Reply #1 - Oct 8th, 2013 at 3:58pm
 
Hi Jae,

They are treated as missing data; this is fairly standard in the field.
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