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    Jaime Huerta-Cepas
    @jhcepas
    then the coordinates of every element in the tree image are monitored to provide interactions
    if using a QtBased GUI, I guess the base tree image could save the space for a QtGraphicsItem used as face, but never tried
    @marco-mariotti when are you planning to start with your project?
    Marco Mariotti
    @marco-mariotti
    @jhcepas I’m a bit reluctant to start on the ETE fork
    the modifications I need to do are mainly in the drawer
    if you plan to replace it, it’d be a bit of a dead end
    could I take a look at the new renderer just to have an idea of how you are doing this now?
    Jaime Huerta-Cepas
    @jhcepas
    not online yet, but I can try to sort my code and show you.
    I just need to solve the problem of large trees. QtGraphics fails on that front
    but, if your plans are just having QtFaces, that could be integrated
    if we stay with the Qt-based GUI
    @marco-mariotti what is exactly what you need to maintain?
    Marco Mariotti
    @marco-mariotti
    at this point I’m pretty much bound to PyQt
    so I need the ete interactive window as PyQt window
    Jaime Huerta-Cepas
    @jhcepas
    that would still be possible, only that interactivity would not come via QtGraphicsItems interactions
    and we could even keep both renderers if necessary.
    Marco Mariotti
    @marco-mariotti
    I could definitively adapt to the new renderer when out
    it’s all up to how difficult it will be to have custom actions/menus for nodes and faces
    Jaime Huerta-Cepas
    @jhcepas
    would be nice to know what are the exact operations/options you use now, so I can keep them in mind while developing the new approach
    Marco Mariotti
    @marco-mariotti
    I’ll send you a summary
    Jaime Huerta-Cepas
    @jhcepas
    cool, thanks
    lexi12
    @lexi12
    I also want to ask if there is an example of the proposal. I think I saw a list of projects from previous years, but there was no link
    Jaime Huerta-Cepas
    @jhcepas
    @lexi12 I cannot find them, but I am sure there were some example for last year
    that's related, not sure if full proposals
    Jaime Huerta-Cepas
    @jhcepas
    proposals are not necessarily long, but need to show that you know you are planning to do. Also, intermediate level in python and linux/git knowledge is necessary, so it is good to support that with examples, or some preliminary interaction with the ETE code
    lexi12
    @lexi12
    Okay, thanks!
    Shaurita D. Hutchins
    @sdhutchins
    is it possible to run ete3 on the command line without doing Slr analysis with codeml? ete3 evol -t data/lysozyme/lysozymeSmall.trees --alg data/lysozyme/lysozymeSmall.txt --model M1
    Shaurita D. Hutchins
    @sdhutchins
    now that I've added the Slr binary, I continue to get the following error File "/usr/local/apps/anaconda3/lib/python3.5/site-packages/ete3/evol/utils.py", line 159, in translate proteinseq += gencode[sequence[n:n+3]] KeyError: 'G'
    I'm guessing it's related to python3.5?
    Francois Serra
    @fransua
    Hi @sdhutchins ,
    related to your first question, I will check... ete3 should be independent from Slr binaries which are getting more and more complicated to install...
    second, I am not sure it is a python3 issue... can you paste/send us the fasta you are using? here or by mail (serra.francois at gmail)?
    thanks
    Bede Constantinides
    @bede
    I'm unable to install ETE3 on OS X at the moment via vanilla Py3.6 or Conda. Any pointers? etetoolkit/ete#285
    Shaurita D. Hutchins
    @sdhutchins
    @fransua I found that some of my alignments were not a multiple of 3 which is a requirement for codeml. Trying to move forward with fixing that, but not sure what the proper process is for clustal omega or if I need to do it manually.
    Francois Serra
    @fransua
    Hi @sdhutchins , perhaps this recipe can help you: http://etetoolkit.org/cookbook/ete_build_mixed_types.ipynb
    Shaurita D. Hutchins
    @sdhutchins
    @fransua thanks for that. It was very helpful. I saw that you guys include iqtree in the etetoolkit on the github repository. Is there a way to presently integrate it?
    Weiqi Feng
    @Weiqi97
    Hi guys, I'm trying to use ete3 within a flask app. On application start up, I got this WARNING: QApplication was not created in the main() thread.
    And QObject::startTimer: Timers can only be used with threads started with QThread
    Eventually, when I render the tree, I would get a empty graph. However, if I run the same code with jupyter notebook, it works just fine.
    Any suggestions? Thanks!
    Samuël Weber/GwendalD
    @weber-s
    Hi! Is this package still maintained? last commit is 7 months old and several PR are wainting.
    Jaime Huerta-Cepas
    @jhcepas
    Yes, it is maintained and updates and new features are under development.
    the team got busier with other issues during the last year, therefore the slow down
    Samuël Weber/GwendalD
    @weber-s
    Ok many thanks! Ete3 is incredibly powerful, thanks for developping it!
    Jaime Huerta-Cepas
    @jhcepas
    sorry about the PRs. We will try to catch up asap.
    Samuël Weber/GwendalD
    @weber-s
    no problem!
    Samuël Weber/GwendalD
    @weber-s
    hello ! Any news for this PR ?
    Jaime Huerta-Cepas
    @jhcepas
    @weber-s just made some comments on your PR
    Samuël Weber/GwendalD
    @weber-s
    Hi! I don't see your comments on the PR.