Problem with getDistanceBetweenAnyTwoNodes

[Mathieu Groussin]

Hi all,
there is a bug with the function getDistanceBetweenAnyTwoNodes...
When I compute the distance between two leaves that are sister-leaves
(they share the same father), the distance is 0, whatever the real
distance between them in the tree.
I know there used to be problems with the getDistanceBetweenAnyTwoNodes
and getPathBetweenAnyTwoNodes a while ago... is it related to this?

Thanks a lot,
Mathieu

[Mathieu Groussin]

Hi again,
Actually, the problem is even worth... all pairwise distances between
leaves are wrong.

Mathieu

[Julien Yann Dutheil]

Hi Matthieu,

Can you fill a report on the bug tracker?

I'll give it a look...

J.

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Julien Y. Dutheil, Ph-D

0 (+49) 4522 763 298

§ Max Planck Institute for Evolutionary Biology

Department of Evolutionary Genetics

Molecular Evolution Group

Plön -- GERMANY

§ Intitute of Evolutionary Sciences - Montpellier
University of Montpellier 2 -- FRANCE

[Mathieu Groussin]

Hi Julien,
yep, I've just done it!
Cheers,
Mathieu

On 8/29/14, 2:51 AM, Julien Yann Dutheil wrote:

Hi Matthieu,

Can you fill a report on the bug tracker?

I'll give it a look...

J.

On Thu, Aug 28, 2014 at 9:59 PM, Mathieu Groussin <mgro...@gmail.com> wrote:

Hi again,
Actually, the problem is even worth... all pairwise distances between leaves are wrong.

Mathieu

On 8/28/14, 3:50 PM, Mathieu Groussin wrote:

Hi all,
there is a bug with the function getDistanceBetweenAnyTwoNodes...
When I compute the distance between two leaves that are sister-leaves (they share the same father), the distance is 0, whatever the real distance between them in the tree.
I know there used to be problems with the getDistanceBetweenAnyTwoNodes and getPathBetweenAnyTwoNodes a while ago... is it related to this?

Thanks a lot,
Mathieu

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Julien Y. Dutheil, Ph-D

0 (+49) 4522 763 298

§ Max Planck Institute for Evolutionary Biology

Department of Evolutionary Genetics

Molecular Evolution Group

Plön -- GERMANY

§ Intitute of Evolutionary Sciences - Montpellier
University of Montpellier 2 -- FRANCE

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[Julien Yann Dutheil]

Hi there,

I have committed a fix to this issue. The bug was actually in getPathBetweenAnyTwoNodes (bug 55). Matthieu, can you check if that indeed solved the problem in your code?

J.

To view this discussion on the web visit https://groups.google.com/d/msgid/biopp-devel-forum/5400CB6F.7020809%40gmail.com.

For more options, visit https://groups.google.com/d/optout.

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Julien Y. Dutheil, Ph-D

0 (+49) 4522 763 298

§ Max Planck Institute for Evolutionary Biology

Molecular Systems Evolution

Department of Evolutionary Genetics