<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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2023-10-28T14:30:27.513Z
2023-10-28T20:14:42.587Z
2023-10-28T20:14:42.587Z
M__
<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>

<phylogenetics><phylogeny><public-databases>
What happened to the PhyLoTA browser?
# 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?

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[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

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## 1 answers

### Answer by username_1 on 2023-10-28. Score: 1

Phylota was implemented in R and is present on GitHub here, described by Bennett et al (2018).
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.


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