Answers.Body: <p>Just to feedback, the GitHub ticket was:</p>
  <blockquote>
  <p><a href="https://github.com/etetoolkit/ete/releases/tag/4.0.0-beta" rel="nofollow noreferrer">ETE4.0.0</a> beta contains an old ETE manual (2009) and a README file for ETE4. Is there an updated ETE4 manual beyond <a href="https://etetoolkit.org/docs/latest/index.html" rel="nofollow noreferrer">etetoolkit.org/docs/latest/index.html</a> or the README of ETE4?</p>
  </blockquote>
  <p>lm-jkominek wrote,</p>
  <blockquote>
  <p>I know it's a bit of necro, but I wanted to second this request  - while the current docs work fine enough for ETE3, they have diverged quite far from ETE4 and there's a bunch of errors that come through when using the latest version that have no explanation...</p>
  </blockquote>
  <p>Thus I'm not alone ... (nothing to do with UAPs BTW)</p>
  <p>jhcepas wrote,</p>
  <blockquote>
  <p>absolutely. We are finishing some final changes to the core of ETE4 and will start with the documentation. In the mean time, @jordibc has a list of most important changes regarding compatibility. Could you share somewhere as a wiki page @jordibc ?</p>
  </blockquote>
  <p>jordibc replied,</p>
  <blockquote>
  <p>Yes, we are working on an updated version of the manual to be released with ete4. In the meantime, most of the old code can be run with some of the changes mentioned in the part of the wiki on migrating from ete3 to ete4. @lm-jkominek and @sarscov2 thanks and hope this helps for the moment!</p>
  </blockquote>
  <p>The GitHub wiki was updated <a href="https://github.com/etetoolkit/ete/wiki/3to4" rel="nofollow noreferrer">here</a>. The Wiki page is kept up to date,</p>
  <blockquote>
  <p>&quot;Jordi Burguet-Castell edited this page 4 days ago · 2 revisions&quot;</p>
  </blockquote>
  <p>The actual additional features (why ETE4 is needed) and how to access them are not listed here. However the changes in syntax are listed. Examples of changes ...</p>
  <pre><code># ETE3
  t = Tree(filename) 
  # ETE4
  t = Tree(open(filename))
  # ETE3
  Tree(name='Hi', dist=1, support=1) 
  # ETE4 
  Tree({'name': 'Hi', 'dist': 1, 'support': 1})
  # ETE3
  Tree(nw, format=1) 
  # ETE4 
  Tree(nw, parser=1)
  </code></pre>
  <p>In summary there's different syntax. So we can start using ETE4</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-12-17T19:22:27.970Z
Answers.Text: thank you very much M__
Answers.UserDisplayName: Andrés Parada
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-09-16T12:53:31.283Z
Answers.LastActivityDate: 2023-09-16T12:53:31.283Z
Answers.UserDisplayName: M__
Body: <p>ETE3 <strong>*</strong> (Environment for Tree Exploration) is a major package and in particular Python package to navigate phylogenetic trees. It is the premier coding library/package for tree manipulation.</p>
  <p>ETE4.0.0 beta has been <a href="https://github.com/etetoolkit/ete/releases/tag/4.0.0-beta" rel="nofollow noreferrer">released</a> via GitHub. The download contains an old ETE manual (2009) and a README file for ETE4, thats about it. Does anyone know the location of the new ETE4 manual, or list of functionality beyond what is in the README (posted below). Reading the code is the last resort ;-)</p>
  <hr />
  <p>README ETE4</p>
  <ul>
  <li>Read and write support for trees in Newick format</li>
  <li>Multiple functions for traversing, searching and manipulating tree topologies and node annotations</li>
  <li>Integration with NCBI Taxonomic database</li>
  <li>Integration with GTDB database</li>
  <li>Programmatic visualization framework</li>
  <li>Visualization of huge trees based on adaptive zooming</li>
  <li>Comparing trees</li>
  <li>Phylogenetic functions:
  <ul>
  <li>orthology detection</li>
  <li>phylogenetic distance?</li>
  </ul>
  </li>
  </ul>
  <hr />
  <p><strong>Reference</strong>
  <strong>*</strong> ETE 3: Reconstruction, analysis and visualization of phylogenomic data.
  Jaime Huerta-Cepas, Francois Serra and Peer Bork.
  Mol Biol Evol 2016; <a href="https://doi:%2010.1093/molbev/msw046" rel="nofollow noreferrer">doi: 10.1093/molbev/msw046</a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-11-17T15:36:11.190Z
Comments.Text: The github page you link to says they have documentation on their official website (http://etetoolkit.org/) and, indeed, clicking on the documentation link there took me to  http://etetoolkit.org/docs/latest/index.html. Is that what you're looking for?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-11-17T16:00:46.903Z
Comments.Text: Thanks @terdon, this is the documentation for ETE Toolkit 3.0.0b34 (last updated Mar 18, 2016). I recognise the ETE3 to ETE4 is small outside phylogenetics, but it is a big upgrade. The authors may respond here, if not I'll send them this link.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-11-17T16:04:05.797Z
Comments.Text: I suspect you will get more traction if you just ask on their github. This isn't a question that is likely to be answerable by anyone other than the devs.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-11-17T16:13:15.637Z
Comments.Text: Good point. https://github.com/etetoolkit/ete/issues/651 ... will pop their response as an answer here. ETE4 has potential.
Comments.UserDisplayName: M__
Tags: <python><phylogenetics><phylogeny><ete3>
Title: ETE4 manual or improved code description
ThreadText: # ETE4 manual or improved code description
  
  (Asked by: username_0 on 2022-11-17)
  
  ETE3 **\*** (Environment for Tree Exploration) is a major package and in particular Python package to navigate phylogenetic trees. It is the premier coding library/package for tree manipulation.
  
  ETE4.0.0 beta has been [released](https://github.com/etetoolkit/ete/releases/tag/4.0.0-beta) via GitHub. The download contains an old ETE manual (2009) and a README file for ETE4, thats about it. Does anyone know the location of the new ETE4 manual, or list of functionality beyond what is in the README (posted below). Reading the code is the last resort ;-)
  
  ---
  
  README ETE4
  
  * Read and write support for trees in Newick format
  * Multiple functions for traversing, searching and manipulating tree topologies and node annotations
  * Integration with NCBI Taxonomic database
  * Integration with GTDB database
  * Programmatic visualization framework
  * Visualization of huge trees based on adaptive zooming
  * Comparing trees
  * Phylogenetic functions:
    + orthology detection
    + phylogenetic distance?
  
  ---
  
  **Reference**
  **\*** ETE 3: Reconstruction, analysis and visualization of phylogenomic data.
  Jaime Huerta-Cepas, Francois Serra and Peer Bork.
  Mol Biol Evol 2016; [doi: 10.1093/molbev/msw046](https://doi:%2010.1093/molbev/msw046)
  
  **Tags:** python, phylogenetics, phylogeny, ete3
  
  > **Comments:**
  > **username_1**: The github page you link to says they have documentation on their official website (http://etetoolkit.org/) and, indeed, clicking on the documentation link there took me to  http://etetoolkit.org/docs/latest/index.html. Is that what you're looking for?  
  > **username_0**: Thanks @username_1, this is the documentation for ETE Toolkit 3.0.0b34 (last updated Mar 18, 2016). I recognise the ETE3 to ETE4 is small outside phylogenetics, but it is a big upgrade. The authors may respond here, if not I'll send them this link.  
  > **username_1**: I suspect you will get more traction if you just ask on their github. This isn't a question that is likely to be answerable by anyone other than the devs.  
  > **username_0**: Good point. https://github.com/etetoolkit/ete/issues/651 ... will pop their response as an answer here. ETE4 has potential.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2023-09-16. Score: 2 | Accepted answer
  
  Just to feedback, the GitHub ticket was:
  
  > [ETE4.0.0](https://github.com/etetoolkit/ete/releases/tag/4.0.0-beta) beta contains an old ETE manual (2009) and a README file for ETE4. Is there an updated ETE4 manual beyond [etetoolkit.org/docs/latest/index.html](https://etetoolkit.org/docs/latest/index.html) or the README of ETE4?
  
  lm-jkominek wrote,
  
  > I know it's a bit of necro, but I wanted to second this request - while the current docs work fine enough for ETE3, they have diverged quite far from ETE4 and there's a bunch of errors that come through when using the latest version that have no explanation...
  
  Thus I'm not alone ... (nothing to do with UAPs BTW)
  
  jhcepas wrote,
  
  > absolutely. We are finishing some final changes to the core of ETE4 and will start with the documentation. In the mean time, @jordibc has a list of most important changes regarding compatibility. Could you share somewhere as a wiki page @jordibc ?
  
  jordibc replied,
  
  > Yes, we are working on an updated version of the manual to be released with ete4. In the meantime, most of the old code can be run with some of the changes mentioned in the part of the wiki on migrating from ete3 to ete4. @lm-jkominek and @sarscov2 thanks and hope this helps for the moment!
  
  The GitHub wiki was updated [here](https://github.com/etetoolkit/ete/wiki/3to4). The Wiki page is kept up to date,
  
  > "Jordi Burguet-Castell edited this page 4 days ago · 2 revisions"
  
  The actual additional features (why ETE4 is needed) and how to access them are not listed here. However the changes in syntax are listed. Examples of changes ...
  
  ```
  # ETE3
  t = Tree(filename) 
  # ETE4
  t = Tree(open(filename))
  # ETE3
  Tree(name='Hi', dist=1, support=1) 
  # ETE4 
  Tree({'name': 'Hi', 'dist': 1, 'support': 1})
  # ETE3
  Tree(nw, format=1) 
  # ETE4 
  Tree(nw, parser=1)
  
  ```
  
  In summary there's different syntax. So we can start using ETE4
  
  > **Comments:**
  > **username_2**: thank you very much M__  
  
  ---
  
  