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A paper I'm reading from 2021[1] mentions doing some analysis on data from the PhyLoTA database, with this reference citation:

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 MBE

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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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