Troubleshooting Sumtrees

Hello everyone, I am a new user of Dendropy, especially bioinformatics computation. i have to summary

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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

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

Listing nearby species

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

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

Custom truncation of GtDB tree

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

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?

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

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

Branch length missing after rerooting

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

Non-equiprobable breaking of polytomies

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

Conversion between DendroPy and ETE3

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

Calculating evolutionary distinctiveness

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

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

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

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

branch lengths to variance co-variance matrix

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

Comments attribute not documented?

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

Fast count of number of nodes

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

Simulating non-ultrametric trees

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

Treatment of unrooted trees

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

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,

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.

Any way to draw a DendroPy tree?

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

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

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

Partitioning taxon sets, missing partition attribute

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

DendroPy 4.4.0 has been released!

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

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: