Tree comparisons

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Tree comparisons

lskatz

Hi, I am comparing two trees with a metric and would like to make a background distribution of random trees. From there I could calculate a Z score and p value.  I thought that the method to do so would involve feeding Tree::RandomFactory isolate names and branch lengths from the original tree. However, this class mutates the branch lengths according to coalescent methods like Yule and does not accept random branch lengths.

So I'm not really sure where to go from there. Should I be using something like Yule to make a background distribution of random trees? Or should I implement a method to take random branch lengths from the original trees?


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Tree comparisons

lskatz

Hi, I am comparing two trees with a metric and would like to make a background distribution of random trees. From there I could calculate a Z score and p value.  I thought that the method to do so would involve feeding Tree::RandomFactory isolate names and branch lengths from the original tree. However, this class mutates the branch lengths according to coalescent methods like Yule and does not accept random branch lengths.

So I'm not really sure where to go from there. Should I be using something like Yule to make a background distribution of random trees? Or should I implement a method to take random branch lengths from the original trees?


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Re: Tree comparisons

Fields, Christopher J
Hi Lee, 

Sorry, been caught up with making changes for the upcoming release.  It’s completely possible this can be accomplished here, but I’m not sure of the best approach within bioperl.  Here’s to hoping my answer will help stimulate further discussion.

chris

On Jun 8, 2016, at 10:32 AM, Lee Katz <[hidden email]> wrote:

Hi, I am comparing two trees with a metric and would like to make a background distribution of random trees. From there I could calculate a Z score and p value.  I thought that the method to do so would involve feeding Tree::RandomFactory isolate names and branch lengths from the original tree. However, this class mutates the branch lengths according to coalescent methods like Yule and does not accept random branch lengths.

So I'm not really sure where to go from there. Should I be using something like Yule to make a background distribution of random trees? Or should I implement a method to take random branch lengths from the original trees?

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