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This forum is for discussing code development with the Bio++ libraries. It is the right place for discussing the library design, or new features to be implemented. It is the wrong place for getting help about the use of the libraries, for this purpose, please check the biopp-help-forum!

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Sergey Chernouhov, Julien Y. Dutheil5

6/27/19

some c++ functions that may be useful?

23.06.2019 update: - Group of function "FindIn" has been updated. - Functions

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some c++ functions that may be useful?

23.06.2019 update: - Group of function "FindIn" has been updated. - Functions

6/27/19

2/22/17

Probelm bpp in installation Phyldog: undefined reference to `bpp

Hello, I am trying to install Phyldog. For that I needed to install bio ++. Howe ever I have these

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Probelm bpp in installation Phyldog: undefined reference to `bpp

Hello, I am trying to install Phyldog. For that I needed to install bio ++. Howe ever I have these

2/22/17

Julien Yann Dutheil, Laurent Guéguen6

4/25/16

Toward a new stable release... (2.3.0) and other news

Portage to C++14 committed on master branch... Please report any trouble! Now compiling with g++6 for

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Toward a new stable release... (2.3.0) and other news

Portage to C++14 committed on master branch... Please report any trouble! Now compiling with g++6 for

4/25/16

Laurent Guéguen, jesse...@gmail.com13

3/3/16

newlik : log computation

Thanks Laurent. This fixed the problem beautifully.

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newlik : log computation

Thanks Laurent. This fixed the problem beautifully.

3/3/16

Thomas Ed. Bigot2

10/2/15

New Graph classes in core

I've just commited 8ed633b in core/master making tree management fully functional (but it must

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New Graph classes in core

I've just commited 8ed633b in core/master making tree management fully functional (but it must

10/2/15

Julien Yann Dutheil

6/29/15

New prog in BppSuite + bpp-popgen dependency

Dear all, Finally... I started a refreshment of the bpp-popgen library. Classes are now structured in

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New prog in BppSuite + bpp-popgen dependency

Dear all, Finally... I started a refreshment of the bpp-popgen library. Classes are now structured in

6/29/15

Duncan Ralph, … Erick Matsen10

4/21/15

Allow different mutation rates to different bases while using per-position mutation rates

Laurent-- You are indeed a nice guy! We owe you many beers, bottles of wine, etc.-- feel free to cash

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Allow different mutation rates to different bases while using per-position mutation rates

Laurent-- You are indeed a nice guy! We owe you many beers, bottles of wine, etc.-- feel free to cash

4/21/15

Julien Yann Dutheil, Laurent Guéguen4

3/31/15

Generic inclusion files (*.all)

Ok, we can do it that way then. A+ L

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Generic inclusion files (*.all)

Ok, we can do it that way then. A+ L

3/31/15

Laurent Guéguen

12/4/14

Aliasable Frequencies Set

Hi folks, now aliasing is possible to/from FrequenciesSet. So it is possible to set as stationary

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Aliasable Frequencies Set

Hi folks, now aliasing is possible to/from FrequenciesSet. So it is possible to set as stationary

12/4/14

Murray Patterson, Julien Yann Dutheil13

11/18/14

SymbolList interface : a question about the design

sounds good! talk to you soon Murray

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SymbolList interface : a question about the design

sounds good! talk to you soon Murray

11/18/14

Laurent Guéguen, Julien Yann Dutheil2

11/18/14

clonable tree Nodes

Definitely fine and needed. I cannot see any issue with that. J.

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clonable tree Nodes

Definitely fine and needed. I cannot see any issue with that. J.

11/18/14

chris warth, Julien Yann Dutheil3

11/1/14

getting bpp project source code?

Oups, I did it again... My mistake, I have again removed a link by mistake on the server while

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getting bpp project source code?

Oups, I did it again... My mistake, I have again removed a link by mistake on the server while

11/1/14

Julien Yann Dutheil2

10/31/14

Version 2.2.0 is there... or almost

Hi there, Just to mention that I finally migrated the full Bio++ website to the wiki. I also

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Version 2.2.0 is there... or almost

Hi there, Just to mention that I finally migrated the full Bio++ website to the wiki. I also

10/31/14

Bastien Boussau, Julien Yann Dutheil8

10/20/14

Hi Bastien, I have updated the corresponding code a bit. I did not find any major issue there though,

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Hi Bastien, I have updated the corresponding code a bit. I did not find any major issue there though,

10/20/14

Mathieu Groussin, Julien Yann Dutheil5

9/17/14

Problem with getDistanceBetweenAnyTwoNodes

Hi there, I have committed a fix to this issue. The bug was actually in getPathBetweenAnyTwoNodes (

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Problem with getDistanceBetweenAnyTwoNodes

Hi there, I have committed a fix to this issue. The bug was actually in getPathBetweenAnyTwoNodes (

9/17/14

Julien Yann Dutheil

9/16/14

An old mystery solved

Hi There, For some versions now the optimization reparametrization option did not lead to accurate

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An old mystery solved

Hi There, For some versions now the optimization reparametrization option did not lead to accurate

9/16/14

Julien Yann Dutheil

8/11/14

Programs user interface, arguments and warnings

Hi, Here is another (too) long email that you most likely do not want to read, but to which I will

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Programs user interface, arguments and warnings

Hi, Here is another (too) long email that you most likely do not want to read, but to which I will

8/11/14

Julien Yann Dutheil

8/11/14

Alphabet states and Model states

Dear all, Here is a small post to clarify some ambiguities in the current version of the libraries,

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Alphabet states and Model states

Dear all, Here is a small post to clarify some ambiguities in the current version of the libraries,

8/11/14

Julien Yann Dutheil2

7/21/14

Server update done!

And BigBrother is back! As space is not a constrain any longer, the nightly compilation was re-

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Server update done!

And BigBrother is back! As space is not a constrain any longer, the nightly compilation was re-

7/21/14

Benoit NABHOLZ, Julien Yann Dutheil2

5/29/14

Ascidian mitochondrial genetic code

Hi Benoit, Fidel actually did that already some time ago. It is on the development version and will

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Ascidian mitochondrial genetic code

Hi Benoit, Fidel actually did that already some time ago. It is on the development version and will

5/29/14

gsw...@g.uky.edu, … Julien Yann Dutheil17

5/16/14

building bio++ on Mavericks

Oups, my mistake, stroke the wrong reply button :D We're still removing those Maverick warnings..

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building bio++ on Mavericks

Oups, my mistake, stroke the wrong reply button :D We're still removing those Maverick warnings..

5/16/14

Connor McCoy, Laurent Guéguen2

5/16/14

WordSubstitutionModel bug

Hi Connor, yes indeed, thanks a lot for the fix, I push it. Cheers, L Le jeudi 15 mai 2014 00:08:06

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WordSubstitutionModel bug

Hi Connor, yes indeed, thanks a lot for the fix, I push it. Cheers, L Le jeudi 15 mai 2014 00:08:06

5/16/14

Julien Yann Dutheil

5/12/14

[To all committers] server update

Dear committers, The current Bio++ server is going on retirement. All accounts are going to be

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[To all committers] server update

Dear committers, The current Bio++ server is going on retirement. All accounts are going to be

5/12/14

gsw...@g.uky.edu

5/2/14

Phylip writer bug

In classic mode, the phylip writer is sending a warning message about possible name truncation to

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Phylip writer bug

In classic mode, the phylip writer is sending a warning message about possible name truncation to

5/2/14

3/12/14

Hello, I reported a bug (pease see http://biopp.univ-montp2.fr/bug/view.php?id=79). This impact many

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Hello, I reported a bug (pease see http://biopp.univ-montp2.fr/bug/view.php?id=79). This impact many

3/12/14

Bastien Boussau, … Nicolas Rochette21

3/7/14

Bug in TreeTemplateTools::midRoot?

I totally agree with the bug detection potential and I also think this should be given priority. But

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Bug in TreeTemplateTools::midRoot?

I totally agree with the bug detection potential and I also think this should be given priority. But

3/7/14

Julien Yann Dutheil

3/6/14

Next stable version

Dear all, This is already one year since the last stable version of Bio++, and it is time for an

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Next stable version

Dear all, This is already one year since the last stable version of Bio++, and it is time for an

3/6/14

Cristian Zambrano, … Julien Yann Dutheil8

3/6/14

Error Compiling with gcc 4.7 -std=c++11

Dear Ikram, Well done, and thanks a lot! Indeed there should be a std:: here, this was clearly an

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Error Compiling with gcc 4.7 -std=c++11

Dear Ikram, Well done, and thanks a lot! Indeed there should be a std:: here, this was clearly an

3/6/14

Ikram, Julien Yann Dutheil3

3/3/14

Using "weighted" sequences for ML computations

You are right, apparently it shouldn't be much of work. Its just that before attempting, I was

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Using "weighted" sequences for ML computations

You are right, apparently it shouldn't be much of work. Its just that before attempting, I was

3/3/14

Thomas BIGOT, Nicolas Rochette2

12/11/13

CMake Find Packages and Bio++

Hi Thomas, This is a good idea that I think has been somewhere on the TODO list for some time.

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CMake Find Packages and Bio++

Hi Thomas, This is a good idea that I think has been somewhere on the TODO list for some time.

12/11/13

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