update_phylota: Update Phylota Clusters

In cromanpa94/rPHYLOTA: Update Phylota Clusters

Description

This function updates a set of phylota clusters using sequences from genbank.

Make sure to have blast installed in your computer (also in your path). For windows users follow the steps outlined in the following link:

https://dmcase.blogspot.com.br/2014/02/how-to-install-blast-on-windows.html

Instructions for MAC users:

https://gist.github.com/knmkr/5393474

In short, this function first download all the available orthologous clusters for a given lineage. Then, it looks for non-overlapping species between the sampled (i.e., PhyloTa) and newly published sequences (i.e., genbank). This function also allows the inclussion of outgroup species.

Each new sequence is then blastes agains each orthologous cluster and merged when a significant match is found. Next, taxonomy is corrected and sampling summaries are exported.

Additional arguments are provided for users interested in performing multiple sequence alignment or using aliscore.

Usage

update_phylota(lineage,nsamples,genes,MSA,ALI,outgroup,correct_db,delete_all,c_directory)

Arguments

lineage	String: A given lineage (e.g. "Sphyraena")
nsamples	numeric: If sequence names are not provided, type the number of sequences to be used when assesing the sequence identity (i.e., more sequence will take more time to process, but the likelihood of ID is higher. I suggest using at least 5)
genes	String: Which genes should the pipeline look for? Use either previous studies to guide yourself or look at PhyloTa database
MSA	Logical: Align sequences?
ALI	Logical: Run Aliscore (only if MSA=T)?
outgroup	String: A vector of strings containing the names of outgroup species
correct_db	Logical: Whether an additional correction step is conducted after the new sequences are included. Subspecies and sp. are removed from the resulting files
delete_all	Logical: Delete all intermediate files
c_directory	Logical: Should the function work in your current working directory?

Value

df	A dataframe containing all the species that were included

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.

Examples

## Not run: 
update_phylota("Alcedinidae",genes=c("RAG-1","ND2"),"Actenoides hombroni",ALI=T,MSA=T,c_directory=T)

## End(Not run)

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