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Google group dedicated to SimPhy users.
SimPhy is a program for the simulation of gene family evolution under incomplete lineage sorting (ILS), gene duplication and loss (GDL), horizontal gene transfer (HGT) and gene conversion (GC).
You can find more information on SimPhy, its sources, manual and example configuration files at GitHub.

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6/30/15

SimPhy 1.0.0 has been released!

You can find the release in the official Github repository of SimPhy https://github.com/adamallo/

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SimPhy 1.0.0 has been released!

You can find the release in the official Github repository of SimPhy https://github.com/adamallo/

6/30/15

Riyad Hossen, Diego Mallo3

7/16/25

Issues with input species tree formatting

Dear Riyad, I suspect you are trying to input the Newick tree file using SimPhy's -s option;

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Issues with input species tree formatting

Dear Riyad, I suspect you are trying to input the Newick tree file using SimPhy's -s option;

7/16/25

zhao shen, Diego M.2

6/29/23

Implications for species tree height

I am glad you are finding SimPhy easy to use. The ST parameter indicates the height of the tree in

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Implications for species tree height

I am glad you are finding SimPhy easy to use. The ST parameter indicates the height of the tree in

6/29/23

Benoit Morel, … Diego M.3

6/29/23

Issue when installing the dependency Math::GSL

Benoit and Noah, thank you for your contributions here! I hope the development of Math::GSL keeps up

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Issue when installing the dependency Math::GSL

Benoit and Noah, thank you for your contributions here! I hope the development of Math::GSL keeps up

6/29/23

maxboys91, Diego M.2

10/12/21

Simulation - Big gene family

Dear Maxime, I am glad you are finding SimPhy useful for your project. Answers to your specific

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Simulation - Big gene family

Dear Maxime, I am glad you are finding SimPhy useful for your project. Answers to your specific

10/12/21

Érico Polo, Diego M.2

7/6/21

-SP needed even when size is informed for every population

Dear Érico, I am glad you are using SimPhy, and I am sorry for this bug you just found. SimPhy

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-SP needed even when size is informed for every population

Dear Érico, I am glad you are using SimPhy, and I am sorry for this bug you just found. SimPhy

7/6/21

Qiuyi Li, Diego M.2

4/26/21

loss rate > duplication rate

Dear Qiuyi, There is a Github branch in SimPhy's repository that deals with this issue. The name

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loss rate > duplication rate

Dear Qiuyi, There is a Github branch in SimPhy's repository that deals with this issue. The name

4/26/21

Qiuyi Li, Diego M.4

4/26/21

length at (above) root?

Dear Qiuyi, Thank you very much for sharing your solution with everyone, and I am sorry I had not

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length at (above) root?

Dear Qiuyi, Thank you very much for sharing your solution with everyone, and I am sorry I had not

4/26/21

siavash mirarab, Diego M.4

11/13/19

Gene trees in unit of generations

Thanks, Diego. On Wed, Nov 13, 2019 at 6:47 PM Diego M. <adam...@gmail.com> wrote: Dear

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Gene trees in unit of generations

Thanks, Diego. On Wed, Nov 13, 2019 at 6:47 PM Diego M. <adam...@gmail.com> wrote: Dear

11/13/19

Elizabeth Allman, Diego M.2

11/12/19

precompiled executables ?

Dear Elizabeth, I am sorry for the late response. You can find the compiled version of SimPhy on the

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precompiled executables ?

Dear Elizabeth, I am sorry for the late response. You can find the compiled version of SimPhy on the

11/12/19

jssd...@gmail.com, Diego M.2

3/22/19

simulate single species with multiple clusters (geographic separation)

I don't fully understand the situation you are describing. Which kind of model would be behind

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simulate single species with multiple clusters (geographic separation)

I don't fully understand the situation you are describing. Which kind of model would be behind

3/22/19

august_guang, Diego M.2

4/27/18

Improper value sampling the parameter -St when set to 1

I am sorry I never answered this. The reason is that you are asking SimPhy to simulate something that

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Improper value sampling the parameter -St when set to 1

I am sorry I never answered this. The reason is that you are asking SimPhy to simulate something that

4/27/18

Érico Polo, Diego M.2

4/27/18

Understanding speciation rate

I am sorry it took me so long to answer. SimPhy simulates species trees using a birth-death process.

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Understanding speciation rate

I am sorry it took me so long to answer. SimPhy simulates species trees using a birth-death process.

4/27/18

Arthur Zwaenepoel, Diego M.5

2/26/18

Death rate higher than birth rate

Hi Diego, I succeeded in building the flexiblesim branch, and it works like a charm. Thanks a bunch!

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Death rate higher than birth rate

Hi Diego, I succeeded in building the flexiblesim branch, and it works like a charm. Thanks a bunch!

2/26/18

Liming Cai, Diego M.2

2/23/18

Simulate locus tree under assumption of whole genome duplication

Dear Liming, I have just realized that this has been waiting here for more than a year. I am very

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Simulate locus tree under assumption of whole genome duplication

Dear Liming, I have just realized that this has been waiting here for more than a year. I am very

2/23/18

Manuel Lafond, Diego M.2

5/27/17

Problems with mapping files

Dear Manuel, Your questions do not directly relate to bugs, but rather to format specifications that

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Problems with mapping files

Dear Manuel, Your questions do not directly relate to bugs, but rather to format specifications that

5/27/17

Erfan Sayyari, … siavash mirarab6

6/29/16

death rate as a function of birth rate

Thanks Diego! If you or someone else decided to implement it, I would suggest using an existing

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death rate as a function of birth rate

Thanks Diego! If you or someone else decided to implement it, I would suggest using an existing

6/29/16

august_guang, Diego M.3

5/11/16

segfault when simulating without leaf constraints and with multiple individuals/species

Thank you very much August, There was a bug indeed. I've already updated the sources. I'll

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segfault when simulating without leaf constraints and with multiple individuals/species

Thank you very much August, There was a bug indeed. I've already updated the sources. I'll

5/11/16

august_guang, Diego M.2

5/11/16

specifying number of rate categories for species-specific heterogeneity

Dear August, The current version of SimPhy does not allow to specify sampling strategies with

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specifying number of rate categories for species-specific heterogeneity

Dear August, The current version of SimPhy does not allow to specify sampling strategies with

5/11/16

Nicholas Crawford, Diego M.8

4/20/16

Modeling migration between specific nodes & RAxML distances.

This is related to my previous answer (I'm sorry for the delay). The tag %4 indicates the HGT

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Modeling migration between specific nodes & RAxML distances.

This is related to my previous answer (I'm sorry for the delay). The tag %4 indicates the HGT

4/20/16

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