DendroPy Users

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11/27/22

Pythonidae data

Hi DendroPy Users, since I 'm new to DendroPy, I would like to know where can I find the data in

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Pythonidae data

Hi DendroPy Users, since I 'm new to DendroPy, I would like to know where can I find the data in

11/27/22

Mark Edward, Jeet Sukumaran2

10/19/21

Compute Edge lengths from external matrix and external tree.`

Does your original tree have edge lengths? On Monday, October 18, 2021 at 6:26:02 PM UTC-7 Mark

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Compute Edge lengths from external matrix and external tree.`

Does your original tree have edge lengths? On Monday, October 18, 2021 at 6:26:02 PM UTC-7 Mark

10/19/21

Aurélien Mazurie, … Davide Cittaro3

9/16/21

Listing nearby species

Hello, was this feature eventually incorporated into dendropy? On Tuesday, December 4, 2012 at 11:52:

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Listing nearby species

Hello, was this feature eventually incorporated into dendropy? On Tuesday, December 4, 2012 at 11:52:

9/16/21

ifreak, Davide Cittaro2

9/16/21

generate a tree from distance matrix inside numpy array

I'm new to dendropy and I realize this message is almost 10y old. Is there any update? The only

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generate a tree from distance matrix inside numpy array

I'm new to dendropy and I realize this message is almost 10y old. Is there any update? The only

9/16/21

Andrzej Zielezinski

9/12/21

Custom truncation of GtDB tree

Dear DendroPy Users, I'm trying to truncate the GtDB tree of Bacteria to retain only selected

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Custom truncation of GtDB tree

Dear DendroPy Users, I'm trying to truncate the GtDB tree of Bacteria to retain only selected

9/12/21

6/25/21

simulating gene trees and sequences within a given species tree

Are there other models, apart from the HKY model, to generate DNA sequences from trees in dendroPy?

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simulating gene trees and sequences within a given species tree

Are there other models, apart from the HKY model, to generate DNA sequences from trees in dendroPy?

6/25/21

Ahmed Elfarargi

11/15/20

The frequency for a particular group across time within a tree

Hi all, I have a Newick tree with multiple lineages, and I need to calculate the frequency of one of

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The frequency for a particular group across time within a tree

Hi all, I have a Newick tree with multiple lineages, and I need to calculate the frequency of one of

11/15/20

Yan Wong, Jeet Sukumaran3

10/20/20

Reporting on number of trees read

Hi Yan Wong, What I do in these cases is to use a tree iterator as opposed to a tree collection. This

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Reporting on number of trees read

Hi Yan Wong, What I do in these cases is to use a tree iterator as opposed to a tree collection. This

10/20/20

Marcos Barbeitos, Jeet Sukumaran11

7/14/20

Branch length missing after rerooting

Hmmm, I see, thanks for the email. It has become obvious that this is not a problem with Dendropy,

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Branch length missing after rerooting

Hmmm, I see, thanks for the email. It has become obvious that this is not a problem with Dendropy,

7/14/20

Yan Wong, mholder3

6/27/20

Non-equiprobable breaking of polytomies

Thanks so much for this Mark. It's really helpful. I'm a little surprised that others hadn

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Non-equiprobable breaking of polytomies

Thanks so much for this Mark. It's really helpful. I'm a little surprised that others hadn

6/27/20

1/13/20

Conversion between DendroPy and ETE3

Hi, I noticed that in the DendroPy interop module, an ete.py script is written for conversion between

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Conversion between DendroPy and ETE3

Hi, I noticed that in the DendroPy interop module, an ete.py script is written for conversion between

1/13/20

10/9/19

Calculating evolutionary distinctiveness

Hi There! I apologize in advance- I'm not an advanced python coder. I do at least have a handle

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Calculating evolutionary distinctiveness

Hi There! I apologize in advance- I'm not an advanced python coder. I do at least have a handle

10/9/19

Liang Xu, Jeet Sukumaran4

7/2/19

How to add character data to the tree for phylogenetic contrasts computation

The speed issue of calculation has been solved. I used multiprocessing to parallelize the computation

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How to add character data to the tree for phylogenetic contrasts computation

The speed issue of calculation has been solved. I used multiprocessing to parallelize the computation

7/2/19

Alexei Kassian, Jeet Sukumaran8

4/1/19

Statistical support for a clade with the exact internal topology

Dear Jeet, thank you. I'll try to follow this way. I also think such a new function, be it added

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Statistical support for a clade with the exact internal topology

Dear Jeet, thank you. I'll try to follow this way. I also think such a new function, be it added

4/1/19

Alexei Kassian, Jeet Sukumaran3

3/28/19

FigTree/Dendroscope cannot read a newick tree generated dy SUMTREES

Dear Jeet, thank you, it works. Just to add: the third option (probably the easiest one) is to

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FigTree/Dendroscope cannot read a newick tree generated dy SUMTREES

Dear Jeet, thank you, it works. Just to add: the third option (probably the easiest one) is to

3/28/19

suman.neu...@gmail.com

2/18/19

branch lengths to variance co-variance matrix

Hi Jeet and everyone, Is there a dendropy function that outputs topology branch lengths to variance

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branch lengths to variance co-variance matrix

Hi Jeet and everyone, Is there a dendropy function that outputs topology branch lengths to variance

2/18/19

Yan Wong, Jeet Sukumaran5

1/29/19

Comments attribute not documented?

Thanks. That's just what I needed to know. I guess others might find it useful if it were

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Comments attribute not documented?

Thanks. That's just what I needed to know. I guess others might find it useful if it were

1/29/19

Yan Wong, … Jeet Sukumaran4

12/29/18

Fast count of number of nodes

As Alexey Morozov notes, you can indeed get the count of nodes through various standard formulae,

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Fast count of number of nodes

As Alexey Morozov notes, you can indeed get the count of nodes through various standard formulae,

12/29/18

sophie....@googlemail.com

10/26/18

Simulating non-ultrametric trees

I'm trying to use dendropy to "build a tree programmatically" as described in (https://

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Simulating non-ultrametric trees

I'm trying to use dendropy to "build a tree programmatically" as described in (https://

10/26/18

krumpelstiltskin, Alexey Morozov6

10/25/18

Treatment of unrooted trees

Things get even stranger when I initialize a tree with a single node. There are now TWO edges! One

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Treatment of unrooted trees

Things get even stranger when I initialize a tree with a single node. There are now TWO edges! One

10/25/18

Michael Matschiner, Jeet Sukumaran3

9/27/18

wrong mrca age when nexus file contains translate block

Thanks a lot, Jeet, for the fast response. Very helpful! Cheers, Michael On Thursday, September 27,

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wrong mrca age when nexus file contains translate block

Thanks a lot, Jeet, for the fast response. Very helpful! Cheers, Michael On Thursday, September 27,

9/27/18

taua...@gmail.com, Jeet Sukumaran2

9/22/18

reroot changes data structure / location of support values

Rooting an unrooted tree is a change in the model. Rerooting a tree is also a change in the model.

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reroot changes data structure / location of support values

Rooting an unrooted tree is a change in the model. Rerooting a tree is also a change in the model.

9/22/18

Alexey Morozov, Jeet Sukumaran4

6/14/18

Any way to draw a DendroPy tree?

DendroPy will output the metadata in a variety of formats with the proper keywords passed to the

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Any way to draw a DendroPy tree?

DendroPy will output the metadata in a variety of formats with the proper keywords passed to the

6/14/18

walz.d...@gmail.com

6/13/18

Simulating contained coalescent trees on ML tree with Bas in substitutions/site

Hello, I'm working on some simulations of reads from genomic data that includes a coalescent

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Simulating contained coalescent trees on ML tree with Bas in substitutions/site

Hello, I'm working on some simulations of reads from genomic data that includes a coalescent

6/13/18

Nathaniel Virgo2

5/29/18

Placing the root at the common ancestor of a clade

After working through this on paper I found a simple solution: I just have to first re-root the tree

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Placing the root at the common ancestor of a clade

After working through this on paper I found a simple solution: I just have to first re-root the tree

5/29/18

Maria Izabel Cavassim Alves, … Paul Maier5

5/25/18

Partitioning taxon sets, missing partition attribute

Nevermind! Figured that one out too: from collections import defaultdict from StringIO import

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Partitioning taxon sets, missing partition attribute

Nevermind! Figured that one out too: from collections import defaultdict from StringIO import

5/25/18

5/7/18

DendroPy 4.4.0 has been released!

2018-05-07 ========== DendroPy 4.4.0 has been released! - Calculation of birth-death likelihoods. -

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DendroPy 4.4.0 has been released!

2018-05-07 ========== DendroPy 4.4.0 has been released! - Calculation of birth-death likelihoods. -

5/7/18

Caleb Ji, Jeet Sukumaran5

1/17/18

Removing taxon with underscore

That works, thank you for your time! On Monday, January 15, 2018 at 9:25:38 AM UTC-8, Caleb Ji wrote:

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Removing taxon with underscore

That works, thank you for your time! On Monday, January 15, 2018 at 9:25:38 AM UTC-8, Caleb Ji wrote:

1/17/18

Erick Matsen, Jeet Sukumaran3

1/17/18

sorting tree branches lexicographically

Jeet-- I think this is exactly what we need! Thanks a ton. Erick On Wed, Jan 17, 2018 at 5:11 AM Jeet

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sorting tree branches lexicographically

Jeet-- I think this is exactly what we need! Thanks a ton. Erick On Wed, Jan 17, 2018 at 5:11 AM Jeet

1/17/18

1/15/18

Hello, I'm currently looking at trying to create a tree dynamically based on Y-DNA SNP mutation

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Hello, I'm currently looking at trying to create a tree dynamically based on Y-DNA SNP mutation

1/15/18

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