Re: Bootstrap, root, reroot...

> To examine rvos' Bio::Phylo was my plan exactly-- Lazy edges can be  
> done I believe, although it seems
> that one of the main reasons to have edges is to
> attach lengths, bootstrap values, etc to them; so we may
> ultimately avoid edge creation only when we construct tree
> topology only--prob rare in practice?
>
> ----- Original Message ----- From: "Chris Fields" <cjfields@...
> >
> To: "Mark A. Jensen" <maj@...>
> Cc: "Aidan Budd" <budd@...>; "BioPerl List" <bioperl-l@...
> >; <tristan.lefebure@...>
> Sent: Wednesday, July 15, 2009 11:29 PM
> Subject: Re: [Bioperl-l] Bootstrap, root, reroot...
>
>
>> I don't; code away.
>>
>> With the edge/branch objects, I'm wondering whether those can be  
>> created lazily (only when needed); it might lighten up the tree a  
>> bit.  Also, don't forget to look at Rutger's Bio::Phylo project,  
>> though I think his modules use inside-out objects (might not be  
>> easy  to work into core unless they are wrapped).
>>
>> chris
>>
>> On Jul 15, 2009, at 4:54 PM, Mark A. Jensen wrote:
>>
>>> After fooling around with bug 2877, I'm thinking seriously about  
>>> starting the edge-branch
>>> project in bioperl-dev, building out an implementation off the  
>>> interfaces B:T:TreeI and B:T:NodeI. It would
>>> give the opp'y for some code rationalization too.
>>> Anyone out there have a problem with that?
>>> cheers MAJ
>>> ----- Original Message ----- From: "Aidan Budd" <budd@...
>>> >
>>> To: "BioPerl List" <bioperl-l@...>
>>> Sent: Saturday, July 11, 2009 3:52 AM
>>> Subject: Re: [Bioperl-l] Bootstrap, root, reroot...
>>>
>>>
>>>> On Thu, 9 Jul 2009, Tristan Lefebure wrote:
>>>>> ...
>>>>> My understanding here is that the problem is linked to the well-  
>>>>> known difficulty to differentiate node from branch labels in  
>>>>> newick trees. Bootstrap scores are branch attributes not node  
>>>>> attributes, but since Bio::TreeI has no branch/edge/bipartition  
>>>>> object they are attached to a node, and in fact reflects the  
>>>>> bootstrap score of the ancestral branch leading to that node.  
>>>>> Troubles naturally come when you are dealing with an unrooted  
>>>>> tree  or reroot a tree: a child can become an ancestor, and, if  
>>>>> the  bootstrap scores is not moved from the old child to the new  
>>>>> child,  it will end up attached at the wrong place (i.e. wrong  
>>>>> node). I  see several fix to that:
>>>>> 1- incorporate Bank's fix into the root() method. I.e. if there  
>>>>> is bootstrap score, after re-rooting, the one on the old to new  
>>>>> ancestor path, should be moved to the right node. 2- Modify the  
>>>>> way trees are stored in bioperl to incorporate branch/edge/  
>>>>> bipartition object, and move the bootstrap scores to them. That  
>>>>> won't be easy and will break many things...
>>>> Just wanted to add that, from my point of view, it would be  
>>>> great  if it
>>>> were possible to add edge/branch objects as part of the bioperl  
>>>> trees. Perhaps so that the previous set of methods still behaved  
>>>> as before, but
>>>> with some new methods on the trees such as get_splits() or  
>>>> get_branches() along with associated split/branch/etc. objects...?
>>>> Being a bioperl user but keeping well away from coding objects  
>>>> in  perl,
>>>> the lack of such methods/objects meant I chose, in the end, not  
>>>> to  use a
>>>> bioperl solution to work with my trees (going instead for a  
>>>> homemade
>>>> clunky python solution, where I'm happier with the OO stuff)
>>>> No idea how difficult/problematic this would be to implement,  
>>>> though - just my 2 cents worth...
>>>>> What do you think?
>>>>> --Tristan
>>>>> _______________________________________________
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>>>> --
>>>> ----------------------------------------------------------------------
>>>> Aidan Budd                                    tel:+49 (0)6221  
>>>> 387  8530
>>>> EMBL - European Molecular Biology Laboratory  fax:+49 (0)6221  
>>>> 387  8517
>>>> Meyerhofstr. 1, 69117 Heidelberg, Germany
>>>> http://www.embl-heidelberg.de/~budd/
>>>> http://www-db.embl.de/jss/EmblGroupsHD/per_1807.html
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>>
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