The ETE toolkit

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This group is intended for solving problems and questions about the use of ETE. Please note that,

Due to spam problems, new users are moderated and first-time messages may take a while to be approved.
Bug reports and feature requests are generally better suited as issues at https://github.com/jhcepas/ete/issues.
A mailing list for developers is available.

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Tatyana Livshultz, dengzi...@gmail.com2

Mar 17

Use ete3 to combine node support values from 2 Newick tree files?

hi! yes, ete3 support tree node annotation so you can modify the node features easily, although # we

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Use ete3 to combine node support values from 2 Newick tree files?

hi! yes, ete3 support tree node annotation so you can modify the node features easily, although # we

Mar 17

JCarlos Villarreal

Mar 17

Getting the gene ID for each node or node of interest

hi ! I am interested in getting the info of gene ID for each node. I have over 200 "genes"

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Getting the gene ID for each node or node of interest

hi ! I am interested in getting the info of gene ID for each node. I have over 200 "genes"

Mar 17

Asuman Inan, dengzi...@gmail.com2

Feb 6

ETE3 not running..

Hi! It seems this is on the server where qt cannot be loaded, please try the following line by add

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ETE3 not running..

Hi! It seems this is on the server where qt cannot be loaded, please try the following line by add

Feb 6

Daniel Fulop, ziqi deng2

Feb 6

Convert ETE tree + data plot into plotly interactive viz?

Hi! Yes! Currently we are advancing toward ete4 where we will engage more with the interactive

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Convert ETE tree + data plot into plotly interactive viz?

Hi! Yes! Currently we are advancing toward ete4 where we will engage more with the interactive

Feb 6

Brittany Baker, dengzi...@gmail.com2

Feb 3

BarChartFace border

hi, so far the papameter of border is not available in the BarChartFace object, but you can change it

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BarChartFace border

hi, so far the papameter of border is not available in the BarChartFace object, but you can change it

Feb 3

Jan 23

Find most recent ancestral node for each tip

Hi, I noticed that the function 't.get_common_ancestor' can give you the first common

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Find most recent ancestral node for each tip

Hi, I noticed that the function 't.get_common_ancestor' can give you the first common

Jan 23

Ziv Lang, dengzi...@gmail.com3

Jan 5

ImportError when running ETE3

Hi, this error occured because it requires PyQt4, please find more information in this thread https:/

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ImportError when running ETE3

Hi, this error occured because it requires PyQt4, please find more information in this thread https:/

Jan 5

Bessem CHOUAIA, ziqi deng3

11/13/22

using a different version of codeml

Dear Ziqi, Thanks for your help. It is finally working. I had to solve a few other problems of

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using a different version of codeml

Dear Ziqi, Thanks for your help. It is finally working. I had to solve a few other problems of

11/13/22

Nitin R, dengzi...@gmail.com2

11/10/22

ValueError: Error parsing Phyml result

Hi! Can you provide the input .faa and cogs file for the run? Best, Ziqi 在2022年10月25日星期二 UTC+2 13:49:

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ValueError: Error parsing Phyml result

Hi! Can you provide the input .faa and cogs file for the run? Best, Ziqi 在2022年10月25日星期二 UTC+2 13:49:

11/10/22

John Allard, dengzi...@gmail.com3

11/10/22

changing branch length scale doesn't seem to work

Hi! Thanks for mentioning this, currently we are moving forward to ete4 which will provide

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changing branch length scale doesn't seem to work

Hi! Thanks for mentioning this, currently we are moving forward to ete4 which will provide

11/10/22

Tatyana Livshultz

11/10/22

script for collapsing nodes based on support?

Hi there: Would someone be willing to share a bit of ete3 code that collapses nodes below a minimum

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script for collapsing nodes based on support?

Hi there: Would someone be willing to share a bit of ete3 code that collapses nodes below a minimum

11/10/22

juan cabrera, dengzi...@gmail.com2

10/25/22

Install problem in mint 20 (ubuntu 20.4)

Hi, this error shows because lack of python-qt. One of the options to install is $ sudo pip install

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Install problem in mint 20 (ubuntu 20.4)

Hi, this error shows because lack of python-qt. One of the options to install is $ sudo pip install

10/25/22

Francesco Cicconardi, Jaime Huerta Cepas2

10/10/22

Node number as in ggtree

Hi francesco, I do not know what ordering preference is used in ggtree. In ETE, you could traverse

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Node number as in ggtree

Hi francesco, I do not know what ordering preference is used in ggtree. In ETE, you could traverse

10/10/22

Minch, Benjamin S, dengzi...@gmail.com2

9/23/22

Having problems getting ete3 to work on Ubuntu

Hi Benjamin, would you mind sharing the errors you encountered? here is the official ete3 install

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Having problems getting ete3 to work on Ubuntu

Hi Benjamin, would you mind sharing the errors you encountered? here is the official ete3 install

9/23/22

8/22/22

Visualization of phylogenetic trees

Hi Ziqi, Trying to plot the sequence alignment as per manual, code from the provided example. I'm

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Visualization of phylogenetic trees

Hi Ziqi, Trying to plot the sequence alignment as per manual, code from the provided example. I'm

8/22/22

8/22/22

SMILES strings as node names

Dear ETE devs, I wanted to use ETE toolkit to create a representation of a tree, where the nodes are

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SMILES strings as node names

Dear ETE devs, I wanted to use ETE toolkit to create a representation of a tree, where the nodes are

8/22/22

8/22/22

Parsing the output

Solved. On Thursday, July 21, 2022 at 3:32:58 PM UTC+2 sunny kevin wrote: Hi Ziqi, How do I parse the

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Parsing the output

Solved. On Thursday, July 21, 2022 at 3:32:58 PM UTC+2 sunny kevin wrote: Hi Ziqi, How do I parse the

8/22/22

Tatyana Livshultz, dengzi...@gmail.com3

8/13/22

very basic: how to run ete3 script on Linux terminal?

Hi Tanya! our example code are mostly python 2 but ete3 is python 3 friendly. so just change the

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very basic: how to run ete3 script on Linux terminal?

Hi Tanya! our example code are mostly python 2 but ete3 is python 3 friendly. so just change the

8/13/22

sunny kevin, dengzi...@gmail.com2

7/19/22

Speeding up the ete3 evol

Hi, the default cpu number of ete3 evol is 1. If you want to increase the speed, you can increase the

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Speeding up the ete3 evol

Hi, the default cpu number of ete3 evol is 1. If you want to increase the speed, you can increase the

7/19/22

sunny kevin, ziqi deng18

7/19/22

ete3 build fails

HI , Trying to run the program with 10 cpus, running from the past ~4 days only 158 /2000 orthologs

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ete3 build fails

HI , Trying to run the program with 10 cpus, running from the past ~4 days only 158 /2000 orthologs

7/19/22

j.j.e.v...@gmail.com

5/16/22

Segmentation fault due to copy('deepcopy') method

Hi all, For some of my analyses, I'm dealing with pretty big gene trees, which I'm annotating

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Segmentation fault due to copy('deepcopy') method

Hi all, For some of my analyses, I'm dealing with pretty big gene trees, which I'm annotating

5/16/22

5/13/22

Coping to errors in concatenated alignments

Hello, I'm trying to run concatenated alignemts throught ETE3 Toolkit from last week but I'm

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Coping to errors in concatenated alignments

Hello, I'm trying to run concatenated alignemts throught ETE3 Toolkit from last week but I'm

5/13/22

5/11/22

M1 Compatibility

Hey, I'm just wondering if ete is compatible with the M1 chip as the anaconda site for

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M1 Compatibility

Hey, I'm just wondering if ete is compatible with the M1 chip as the anaconda site for

5/11/22

Sharon Elaine D'Souza

4/8/22

Request for help

Can someone please help me? I keep on getting this error: error in sequence data file: l at 1 seq 1.

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Request for help

Can someone please help me? I keep on getting this error: error in sequence data file: l at 1 seq 1.

4/8/22

石川昌和, ziqi deng2

3/29/22

Error when I try to write tree

Hi! the workflow standard_raxml is set to process unaligned sequence. In your case, you already have

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Error when I try to write tree

Hi! the workflow standard_raxml is set to process unaligned sequence. In your case, you already have

3/29/22

Arafat Rahman, … François Serrra9

3/25/22

KeyError ''lnL'

the number of sequences costs more than their length, and you have 264... I personally never tried

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KeyError ''lnL'

the number of sequences costs more than their length, and you have 264... I personally never tried

3/25/22

Alexander Bradshaw, dengzi...@gmail.com2

3/4/22

c_iqtree_codon_bestmodel

Hi, here are the infos of above workflows c_iqtree_bestmodel = clustalo_default-none-none-

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c_iqtree_codon_bestmodel

Hi, here are the infos of above workflows c_iqtree_bestmodel = clustalo_default-none-none-

3/4/22

Luigi Faino, fransua2

2/25/22

Hi Luigi, this is the result of running a site model. A simple example can be found there: http://

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Hi Luigi, this is the result of running a site model. A simple example can be found there: http://

2/25/22

Mariane Brom Sobreiro

2/18/22

ETE3 for all users on a server

Hello everyone! How are you? I currently manage a Linux server and I would like to make ETE3

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ETE3 for all users on a server

Hello everyone! How are you? I currently manage a Linux server and I would like to make ETE3

2/18/22

Courtney Stairs, … Courtney Stairs3

2/1/22

ete3 install error from conda etetoolkit channel :(

Wow - yep that worked. Thanks a lot. Past Courtney really wished she tried this earlier... Super

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ete3 install error from conda etetoolkit channel :(

Wow - yep that worked. Thanks a lot. Past Courtney really wished she tried this earlier... Super

2/1/22

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