Groups
Conversations
All groups and messages
Send feedback to Google
Help
Training
Sign in
Groups
The ETE toolkit
Conversations
Labels
About
Groups keyboard shortcuts have been updated
Dismiss
See shortcuts
The ETE toolkit
Contact owners and managers
1–30 of 633
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.
Mark all as read
Report group
0 selected
Claudia Marcela Ortiz Sepulveda
, …
Adrian Pelin
3
10/2/24
Error after ete3 evol using model SLR
This error " double free or corruption (out) " seems to appear from time to time (10-20% of
unread,
Error after ete3 evol using model SLR
This error " double free or corruption (out) " seems to appear from time to time (10-20% of
10/2/24
Vishal Joshi
, …
dengzi...@gmail.com
7
8/27/24
NCBI taxonomy failing to download
Hi! I understand! Let me get back to you once we updated! Best, Ziqi 在2024年8月19日星期一 UTC+2 16:30:33
unread,
NCBI taxonomy failing to download
Hi! I understand! Let me get back to you once we updated! Best, Ziqi 在2024年8月19日星期一 UTC+2 16:30:33
8/27/24
Marc Hoeppner
8/26/24
Label subtrees based on broader taxonomic classifications
Hi, I have the following task - which I am not sure how to solve within ete. Basically, I want to
unread,
Label subtrees based on broader taxonomic classifications
Hi, I have the following task - which I am not sure how to solve within ete. Basically, I want to
8/26/24
Bertrand Cornu
8/22/24
Branches too far from the leaves in circular tree
In this script, I specify species that meet a given criterion. However, the display of the circular
unread,
Branches too far from the leaves in circular tree
In this script, I specify species that meet a given criterion. However, the display of the circular
8/22/24
Marc Hoeppner
2
7/5/24
Ete3 - get subtree from NCBI with names as labels
After more Googling, I found that I have to rename each leaf individually. Works now On Friday 5 July
unread,
Ete3 - get subtree from NCBI with names as labels
After more Googling, I found that I have to rename each leaf individually. Works now On Friday 5 July
7/5/24
Elisa Josefa González Ugalde
5/6/24
How to interpret the results for branch-site in ete-evol?
Hello to the entire ete3 community! I'm new here, I'm very sorry if this question has already
unread,
How to interpret the results for branch-site in ete-evol?
Hello to the entire ete3 community! I'm new here, I'm very sorry if this question has already
5/6/24
Adam
,
dengzi...@gmail.com
3
5/6/24
using ete3 with newer python versions
Thanks. That worked. On Fri, Apr 26, 2024 at 10:35 AM dengzi...@gmail.com <dengzi...@gmail.com
unread,
using ete3 with newer python versions
Thanks. That worked. On Fri, Apr 26, 2024 at 10:35 AM dengzi...@gmail.com <dengzi...@gmail.com
5/6/24
David Weng
, …
Brittany Baker
5
4/17/24
M1 Compatibility
Hi, Thank you very much for your quick reply. I didn't realize the basic ete3 tools work without
unread,
M1 Compatibility
Hi, Thank you very much for your quick reply. I didn't realize the basic ete3 tools work without
4/17/24
Will Fulton
2/7/24
How to display node names at all Levels?
Hello, I have searched everywhere, but I cannot find a way to create a graph that shows the node name
unread,
How to display node names at all Levels?
Hello, I have searched everywhere, but I cannot find a way to create a graph that shows the node name
2/7/24
Yogesh Sharma
2/3/24
recolour the alignment on the basis of percentage identity
hi i am trying to make a figure with phylotree and MSA. but i am facing some issues 1) phylogentic
unread,
recolour the alignment on the basis of percentage identity
hi i am trying to make a figure with phylotree and MSA. but i am facing some issues 1) phylogentic
2/3/24
Yogesh Sharma
2/3/24
display alignment next to tree
hi i am new to ete3 i want to make a representation somewhat like the one displayed here http://
unread,
display alignment next to tree
hi i am new to ete3 i want to make a representation somewhat like the one displayed here http://
2/3/24
Elizaveta Kazakova
,
dengzi...@gmail.com
2
2/1/24
ete3 version 3.1.3 issue
Hi Elizaveta! Thanks for the kind word! The method get_descdendant_taxa() will get the descendant
unread,
ete3 version 3.1.3 issue
Hi Elizaveta! Thanks for the kind word! The method get_descdendant_taxa() will get the descendant
2/1/24
Konnaris, Maxwell
12/4/23
support
Hi, Im trying to use ETE4 to create a tree of life representation, much like the one you have
unread,
support
Hi, Im trying to use ETE4 to create a tree of life representation, much like the one you have
12/4/23
Michael Gruenstaeudl
11/27/23
How to visualize mixed sequence alignment via PhyloTree
I am looking for a way to visualize a mixed sequence alignment - comprising of DNA nucleotides as
unread,
How to visualize mixed sequence alignment via PhyloTree
I am looking for a way to visualize a mixed sequence alignment - comprising of DNA nucleotides as
11/27/23
Michael Gruenstaeudl
2
11/27/23
Leaf names visible despite show_leaf_name=False
A simple, albeit unconventional solution would be to replace the original leaf name with an empty
unread,
Leaf names visible despite show_leaf_name=False
A simple, albeit unconventional solution would be to replace the original leaf name with an empty
11/27/23
Wesley Johnston
,
dengzi...@gmail.com
2
11/26/23
Input file populates upload box but Show tree generates bacteria tree
Were you trying on the http://etetoolkit.org/treeview/? If yes, it's just a experimental version.
unread,
Input file populates upload box but Show tree generates bacteria tree
Were you trying on the http://etetoolkit.org/treeview/? If yes, it's just a experimental version.
11/26/23
lcscs...@gmail.com
, …
dengzi...@gmail.com
9
11/26/23
Non-standard genetic code
Thanks for your reply! I will look into it Best, Ziqi 在2023年11月8日星期三 UTC+1 15:48:08<jrichar...@
unread,
Non-standard genetic code
Thanks for your reply! I will look into it Best, Ziqi 在2023年11月8日星期三 UTC+1 15:48:08<jrichar...@
11/26/23
许东
,
dengzi...@gmail.com
2
11/6/23
Legend issue about ete3
Hi! Sorry for the late response as we are currently upgrating ete3 to ete4. In ete4 we adopt a new
unread,
Legend issue about ete3
Hi! Sorry for the late response as we are currently upgrating ete3 to ete4. In ete4 we adopt a new
11/6/23
Heather Onorati
,
dengzi...@gmail.com
2
10/9/23
Phylogenetic tree viewer - download image?
Hi! I guess you refered to http://etetoolkit.org/treeview/. It has been the demo version for years,
unread,
Phylogenetic tree viewer - download image?
Hi! I guess you refered to http://etetoolkit.org/treeview/. It has been the demo version for years,
10/9/23
Margaux Jullien
8/23/23
Plot a tree with a heatmap
Hello, I would like to build a tree representation next to a heatmap of the sequence identity matrix
unread,
Plot a tree with a heatmap
Hello, I would like to build a tree representation next to a heatmap of the sequence identity matrix
8/23/23
Kitty Murphy
,
dengzi...@gmail.com
2
8/9/23
Stop codons
Hi Kitty, sorry for such a slow reply. As far as I am concerned, ete evol module doesn't have any
unread,
Stop codons
Hi Kitty, sorry for such a slow reply. As far as I am concerned, ete evol module doesn't have any
8/9/23
Alexandre Flageul
,
ziqi deng
2
4/20/23
Could not load the Qt platform plugin "xcb" in "" even though it was found
Hello! I see, this error often happens could be because during deploy software, it doesn't deploy
unread,
Could not load the Qt platform plugin "xcb" in "" even though it was found
Hello! I see, this error often happens could be because during deploy software, it doesn't deploy
4/20/23
Amit Rai
,
dengzi...@gmail.com
2
4/11/23
request for your help to install ete3
Hi! I noticed your python version is 3.9. It could be because of pmodeltest, a tool in ete3_toolchain
unread,
request for your help to install ete3
Hi! I noticed your python version is 3.9. It could be because of pmodeltest, a tool in ete3_toolchain
4/11/23
Tatyana Livshultz
,
dengzi...@gmail.com
2
3/17/23
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
unread,
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
3/17/23
JCarlos Villarreal
3/17/23
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"
unread,
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"
3/17/23
Asuman Inan
,
dengzi...@gmail.com
2
2/6/23
ETE3 not running..
Hi! It seems this is on the server where qt cannot be loaded, please try the following line by add
unread,
ETE3 not running..
Hi! It seems this is on the server where qt cannot be loaded, please try the following line by add
2/6/23
Daniel Fulop
,
ziqi deng
2
2/6/23
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
unread,
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
2/6/23
Brittany Baker
,
dengzi...@gmail.com
2
2/3/23
BarChartFace border
hi, so far the papameter of border is not available in the BarChartFace object, but you can change it
unread,
BarChartFace border
hi, so far the papameter of border is not available in the BarChartFace object, but you can change it
2/3/23
Santi Montero
1/23/23
Find most recent ancestral node for each tip
Hi, I noticed that the function 't.get_common_ancestor' can give you the first common
unread,
Find most recent ancestral node for each tip
Hi, I noticed that the function 't.get_common_ancestor' can give you the first common
1/23/23
Ziv Lang
,
dengzi...@gmail.com
3
1/5/23
ImportError when running ETE3
Hi, this error occured because it requires PyQt4, please find more information in this thread https:/
unread,
ImportError when running ETE3
Hi, this error occured because it requires PyQt4, please find more information in this thread https:/
1/5/23