get_PHYLOTA: Download PHYLOTA clusters

In cromanpa94/rPHYLOTA: Update Phylota Clusters

Description

This function retrieves all PHYLOTA clusters for a given clade. Make sure that there are informative clusters in the database. Otherwise it will not work. This function (1) creates a new folder in your working directory, and (2) saves each cluster into a fasta format file.

Two additional arguments were included into the function to (1) perform multiple sequence alignment of each orthologous cluster and (2) run aliscore on the same set.

I suggest using SuperMatrix function (evobioR package) to concatenate MSAs.

Usage

get_PHYLOTA(clade,MSA=FALSE, ALI=FALSE, c_directory=FALSE)

Arguments

clade	String: Lineage name (e.g. "Sphyraena")
MSA	Logical: Perform a MSA on the clusters (only ClustalOmega available)
ALI	Logical: Run Aliscore on the MSA
c_directory	Logical: Should the function work in your current working directory?

Details

Please select a single clade. No

Author(s)

Cristian Roman-Palacios

References

Sanderson, M. J., Boss, D., Chen, D., Cranston, K. A., & Wehe, A. (2008). The PhyLoTA Browser: processing GenBank for molecular phylogenetics research. Systematic Biology, 57(3), 335-346.

Misof, B., & Misof, K. (2009). A Monte Carlo approach successfully identifies randomness in multiple sequence alignments: a more objective means of data exclusion. Systematic biology, 58(1), 21-34.

Sievers, F., & Higgins, D. G. (2014). Clustal Omega, accurate alignment of very large numbers of sequences. Multiple sequence alignment methods, 105-116.

Examples

## Not run: 
 get_PHYLOTA("Sphyraena", MSA=TRUE, ALI=TRUE, c_directory=T)
 
## End(Not run)

cromanpa94/rPHYLOTA documentation built on Nov. 4, 2019, 9:18 a.m.