Talk to phylo software and servers

[DomBennett]

Possible R packages to fill this niche:

• https://cran.r-project.org/web/packages/ips/ips.pdf
• https://bioconductor.org/packages/3.7/bioc/vignettes/msa/inst/doc/msa.pdf

[rvosa]

The CIPRES REST API gives access to muscle, mafft and raxml, besides a lot of others (including Bayesian tools). It would be pretty amazing if we would just use that and dispose of local command line dependencies: https://www.phylo.org/restusers/docs/tools