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David Weng
, …
Brittany Baker
5
6:12 AM
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
6:12 AM
Vishal Joshi
,
ziqi deng
4
Mar 27
NCBI taxonomy failing to download
Hi Vishal, we have already released in our main branch actually. ETE Toolkit has already updated to
unread,
NCBI taxonomy failing to download
Hi Vishal, we have already released in our main branch actually. ETE Toolkit has already updated to
Mar 27
Will Fulton
Feb 7
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
Feb 7
Yogesh Sharma
Feb 3
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
Feb 3
Yogesh Sharma
Feb 3
display alignment next to tree
hi i am new to ete3 i want to make a representation somewhat like the one displayed here http://
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display alignment next to tree
hi i am new to ete3 i want to make a representation somewhat like the one displayed here http://
Feb 3
Elizaveta Kazakova
,
dengzi...@gmail.com
2
Feb 1
ete3 version 3.1.3 issue
Hi Elizaveta! Thanks for the kind word! The method get_descdendant_taxa() will get the descendant
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ete3 version 3.1.3 issue
Hi Elizaveta! Thanks for the kind word! The method get_descdendant_taxa() will get the descendant
Feb 1
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
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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
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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,
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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
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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
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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"
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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"
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
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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
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
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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
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
Bessem CHOUAIA
,
ziqi deng
3
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
unread,
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.com
2
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.com
3
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
unread,
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
unread,
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.com
2
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
unread,
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 Cepas
2
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
unread,
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