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Bio++ Usage Help Forum

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Welcome to the Bio++ Usage Help Forum.

You can post a message if you need help on using the Bio++ libraries (http://biopp.univ-montp2.fr/).

The Bio++ development team.

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Julien Yann Dutheil

3/3/15

A survey for future development of Bio++

Dear Bio++ users, I made a small survey to collect informations on users experience with Bio++. It

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A survey for future development of Bio++

Dear Bio++ users, I made a small survey to collect informations on users experience with Bio++. It

3/3/15

Alex A, Julien Y. Dutheil3

1/12/22

getting started

Hi Alex, First, I have to apologize as the current status of Bio++ is a bit messy: we are in the

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getting started

Hi Alex, First, I have to apologize as the current status of Bio++ is a bit messy: we are in the

1/12/22

elsemikk, Laurent Guéguen7

9/22/21

Hi Else, could you show your config files, please? Cheers, Laurent Le lundi 20 septembre 2021 à 07:54

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Hi Else, could you show your config files, please? Cheers, Laurent Le lundi 20 septembre 2021 à 07:54

9/22/21

omotoso olatunde, Julien Y. Dutheil3

5/20/21

VectorSiteContainer::getSequencePosition()

Thank you @Professor Julien, you were right, some names were modified by the Time Tree that I forgot

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VectorSiteContainer::getSequencePosition()

Thank you @Professor Julien, you were right, some names were modified by the Time Tree that I forgot

5/20/21

lwang....@gmail.com, … Julien Y. Dutheil6

10/15/20

how to set HIVw+R6 substitution model in bppsuite?

Dear Liang, See http://biopp.univ-montp2.fr/manual/html/bppsuite/2.4.0/bppsuite.html#Protein, the

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how to set HIVw+R6 substitution model in bppsuite?

Dear Liang, See http://biopp.univ-montp2.fr/manual/html/bppsuite/2.4.0/bppsuite.html#Protein, the

10/15/20

Keren Halabi, … Julien Y. Dutheil3

8/12/20

UserAlphabetIndex1: incorrect usage not halted?

Hi, This is strange, this minus 1 was not part of the original class, it was introduced later on...

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UserAlphabetIndex1: incorrect usage not halted?

Hi, This is strange, this minus 1 was not part of the original class, it was introduced later on...

8/12/20

Keren Halabi, Laurent Guéguen3

8/12/20

MixedSustitutionModelSet - division by 0

Thank you for the quick and elaborated response! If I understand correctly, this standardization is

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MixedSustitutionModelSet - division by 0

Thank you for the quick and elaborated response! If I understand correctly, this standardization is

8/12/20

Keren Halabi, Laurent Guéguen2

8/12/20

Two memory leaks

Hi Keren, since newlikelihood is currently under development, there is no need to fix this issue in

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Two memory leaks

Hi Keren, since newlikelihood is currently under development, there is no need to fix this issue in

8/12/20

Keren Halabi, Laurent Guéguen2

8/12/20

A general non-homogeneous model with one path that allows all combinations vs. a one_per_branch model

Hi Keren, I agree that the 1st implementation is not easy, since you would have to alias all omegas

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A general non-homogeneous model with one path that allows all combinations vs. a one_per_branch model

Hi Keren, I agree that the 1st implementation is not easy, since you would have to alias all omegas

8/12/20

Keren Halabi, Laurent Guéguen3

1/21/20

Adding feature - customization of nucleotide substitution model in YN98 class

Thank you, Laurent! This is exactly what I needed. Cheers, Keren

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Adding feature - customization of nucleotide substitution model in YN98 class

Thank you, Laurent! This is exactly what I needed. Cheers, Keren

1/21/20

Keren Halabi, Julien Y. Dutheil8

12/5/19

Access to Bio++ wiki

Hi dear Julien, I suspect this is happening again. Cheers, Keren

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Access to Bio++ wiki

Hi dear Julien, I suspect this is happening again. Cheers, Keren

12/5/19

Keren Halabi, Laurent Guéguen14

11/25/19

Likelihood computation - (homogeneous) site model vs. (non-homogeneous) branch-site model with custom restrictions

Hi, thanks to Keren who found the bug, the problem is solved. Cheers, Laurent

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Likelihood computation - (homogeneous) site model vs. (non-homogeneous) branch-site model with custom restrictions

Hi, thanks to Keren who found the bug, the problem is solved. Cheers, Laurent

11/25/19

Liang Wang, Julien Y. Dutheil3

11/4/19

config file error?

Hi Julien: Thank you for your patience. I just commet the output.tree_ids.file, and also modified the

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config file error?

Hi Julien: Thank you for your patience. I just commet the output.tree_ids.file, and also modified the

11/4/19

Keren Halabi, Laurent Guéguen3

8/30/19

YNGP_M3 model fitting erorr

Thanks Laurent! I will make sure to sync these into my fork. Keren

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YNGP_M3 model fitting erorr

Thanks Laurent! I will make sure to sync these into my fork. Keren

8/30/19

Keren Halabi, Laurent Guéguen2

8/21/19

Implementation of triple mixture model

Hi Keren, I took some time to think about it, and to my opinion the best possible way would be the

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Implementation of triple mixture model

Hi Keren, I took some time to think about it, and to my opinion the best possible way would be the

8/21/19

Liang Wang, … Julien Y. Dutheil9

8/19/19

ancestral sequence reconstruction

Dear Julien, Your suggestion is very helpful to me. I will practice it immediately.

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ancestral sequence reconstruction

Dear Julien, Your suggestion is very helpful to me. I will practice it immediately.

8/19/19

Liang Wang, Laurent Guéguen3

8/17/19

reconstrution of acenstral viral sequences

Dear Laurent, Thank you for your patience. I will try to proceed with your advice. Best wishes!

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reconstrution of acenstral viral sequences

Dear Laurent, Thank you for your patience. I will try to proceed with your advice. Best wishes!

8/17/19

Keren Halabi, Laurent Guéguen5

6/19/19

Customizing the constraint on the omega parameter of YN98

Dear Keren, it is possible if you change the limits in the source code in YN98.cpp. The 0.001 limit

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Customizing the constraint on the omega parameter of YN98

Dear Keren, it is possible if you change the limits in the source code in YN98.cpp. The 0.001 limit

6/19/19

Keren Halabi, Laurent Guéguen6

6/18/19

Alter the constraint of an aliased parameter

Dear Keren, you should go on with devel branches now. Cheers, laurent

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Alter the constraint of an aliased parameter

Dear Keren, you should go on with devel branches now. Cheers, laurent

6/18/19

Keren Halabi, Laurent Guéguen7

6/18/19

UserAlphabetIndex1::getIndex() exceed boundaries of index_ data member

Dear Keren, sorry for the delay, I am rather busy these days. Indeed, little bug in Binary, it should

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UserAlphabetIndex1::getIndex() exceed boundaries of index_ data member

Dear Keren, sorry for the delay, I am rather busy these days. Indeed, little bug in Binary, it should

6/18/19

Keren Halabi, Laurent Guéguen11

6/10/19

Question about probabilistic mapping

Thank you, Laurent! Now everything is clear to me. Cheers, Keren

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Question about probabilistic mapping

Thank you, Laurent! Now everything is clear to me. Cheers, Keren

6/10/19

Benoit N, Julien Y. Dutheil2

5/20/19

Popgen documentation

Thanks Benoit, will give it a look asap. In the meantime, you can get the latest one here: http://

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Popgen documentation

Thanks Benoit, will give it a look asap. In the meantime, you can get the latest one here: http://

5/20/19

Keren Halabi, Laurent Guéguen3

5/15/19

getPij of class AbstractSubstitutionModel

Hi Laurent, Sorry for the delay and thank you for the clarification! Cheers, Keren

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getPij of class AbstractSubstitutionModel

Hi Laurent, Sorry for the delay and thank you for the clarification! Cheers, Keren

5/15/19

Keren Halabi, Julien Y. Dutheil7

5/12/19

OneDimensionOptimizationTools::bracketMinimum - clarification on line 93

Hi Julien, It's not a problem. Thank you for the elaborated answer. I have pulled request (#19).

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OneDimensionOptimizationTools::bracketMinimum - clarification on line 93

Hi Julien, It's not a problem. Thank you for the elaborated answer. I have pulled request (#19).

5/12/19

Keren Halabi, Laurent Guéguen4

4/8/19

Assign a parameter to multiple functions

Dear Keren, yes indeed, ParameterListeners are only used to alias different parameters, for example

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Assign a parameter to multiple functions

Dear Keren, yes indeed, ParameterListeners are only used to alias different parameters, for example

4/8/19

Keren Halabi, Laurent Guéguen2

12/17/18

Codon model based on GTR nucleotide matrix

Hi Keren, this is possible, and the syntax is bpp specific, since YN98 is specifically used for the

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Codon model based on GTR nucleotide matrix

Hi Keren, this is possible, and the syntax is bpp specific, since YN98 is specifically used for the

12/17/18

Keren Halabi, Laurent Guéguen2

12/10/18

Non-homogenous one per branch model likelihood computation

Hi Keren, I am sorry for the mislead, but this description is false; it is the remain of a previous

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Non-homogenous one per branch model likelihood computation

Hi Keren, I am sorry for the mislead, but this description is false; it is the remain of a previous

12/10/18

Keren Halabi, … Laurent Guéguen5

12/6/18

Discrepancy in likelihood values between PAML and Bio++ for M2 model

Hi Keren, we did not implement the CF3X4 correction, because in my point of view this correction is

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Discrepancy in likelihood values between PAML and Bio++ for M2 model

Hi Keren, we did not implement the CF3X4 correction, because in my point of view this correction is

12/6/18

Keren Halabi, Laurent Guéguen7

11/8/18

Likelihood computation for multiple sites in parallel

Dear Laurent, Indeed, the usage of OpenMP is both easier to use and allows additional features such

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Likelihood computation for multiple sites in parallel

Dear Laurent, Indeed, the usage of OpenMP is both easier to use and allows additional features such

11/8/18

Keren Halabi, Laurent Guéguen6

11/5/18

nonohomogenous one_per_branch setting - how to alias based on branch ID?

Dear Keren, all new developments related to the classic likelihood computation are on the devel

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nonohomogenous one_per_branch setting - how to alias based on branch ID?

Dear Keren, all new developments related to the classic likelihood computation are on the devel

11/5/18

Михаил Щелкунов, Laurent Guéguen2

10/20/18

Are branch lengths measured in substitutions/codon or substitutions/base pair?

Hello, they are in substitutions per site, where the "site" nature depends on the model.

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Are branch lengths measured in substitutions/codon or substitutions/base pair?

Hello, they are in substitutions per site, where the "site" nature depends on the model.

10/20/18

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