Answers.Body: <p>Phylota was implemented in R and is present on <a href="https://github.com/ropensci/phylotaR" rel="nofollow noreferrer">GitHub here</a>, described by <a href="https://doi.org/10.3390/life8020020" rel="nofollow noreferrer">Bennett <em>et al</em> (2018)</a>.</p>
  <p>Here's the code...</p>
  <pre><code>library(phylotaR)
  wd &lt;- '[FILEPATH TO WORKING DIRECTORY]'
  ncbi_dr &lt;- '[FILEPATH TO COMPILED BLAST+ TOOLS]'
  txid &lt;- 9443  # primates ID
  setup(wd = wd, txid = txid, ncbi_dr = ncbi_dr)
  run(wd = wd)
  </code></pre>
  <p>Sanderson <em>et al</em>  was 15 years ago, albeit Sys. Biol. is a very reputable journal in phylogenetics. I've deployed solutions published there with outstanding results.</p>
  
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Answers.CreationDate: 2023-10-28T14:30:27.513Z
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Body: <p>A paper I'm reading from 2021<sup>[1]</sup> mentions doing some analysis on data from the PhyLoTA database, with this reference citation:</p>
  <ul>
  <li>M. J. Sanderson et. al. 2008 <a href="https://doi.org/10.1080/10635150802158688" rel="nofollow noreferrer">The PhyLoTa Browser: processing GenBank for molecular phylogenetics research</a>, <em>Syst. Biol.</em> 57(3) 335-346.</li>
  </ul>
  <p>This paper abstract claims to have an online interface at <a href="http://loco.biosci.arizona.edu/pb" rel="nofollow noreferrer">http://loco.biosci.arizona.edu/pb</a>, but this link is not currently responsive. Does anyone know what happened to this project, and if it is currently accessible at some other location?</p>
  <hr />
  <p>[1] S. M. Harrington et. al. 2021 <a href="https://doi.org/10.1093/molbev/msaa295" rel="nofollow noreferrer">Properties of Markov chain Monte Carlo performance across many empirial alignments</a> MBE</p>
  
Tags: <phylogenetics><phylogeny><public-databases>
Title: What happened to the PhyLoTA browser?
ThreadText: # What happened to the PhyLoTA browser?
  
  (Asked by: username_0 on 2023-10-27)
  
  A paper I'm reading from 2021[1] mentions doing some analysis on data from the PhyLoTA database, with this reference citation:
  
  * M. J. Sanderson et. al. 2008 [The PhyLoTa Browser: processing GenBank for molecular phylogenetics research](https://doi.org/10.1080/10635150802158688), *Syst. Biol.* 57(3) 335-346.
  
  This paper abstract claims to have an online interface at <http://loco.biosci.arizona.edu/pb>, but this link is not currently responsive. Does anyone know what happened to this project, and if it is currently accessible at some other location?
  
  ---
  
  [1] S. M. Harrington et. al. 2021 [Properties of Markov chain Monte Carlo performance across many empirial alignments](https://doi.org/10.1093/molbev/msaa295) MBE
  
  **Tags:** phylogenetics, phylogeny, public-databases
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2023-10-28. Score: 1
  
  Phylota was implemented in R and is present on [GitHub here](https://github.com/ropensci/phylotaR), described by [Bennett *et al* (2018)](https://doi.org/10.3390/life8020020).
  
  Here's the code...
  
  ```
  library(phylotaR)
  wd <- '[FILEPATH TO WORKING DIRECTORY]'
  ncbi_dr <- '[FILEPATH TO COMPILED BLAST+ TOOLS]'
  txid <- 9443  # primates ID
  setup(wd = wd, txid = txid, ncbi_dr = ncbi_dr)
  run(wd = wd)
  
  ```
  
  Sanderson *et al* was 15 years ago, albeit Sys. Biol. is a very reputable journal in phylogenetics. I've deployed solutions published there with outstanding results.
  
  
  ---
  
  