extract_alignment: Download MalAvi Sequence Alignments

In vincenzoaellis/malaviR: An R interface to MalAvi

Description

This function downloads the three sequence alignment files available on the MalAvi website.

Usage

extract_alignment(alignment = "all seqs")

Arguments

alignment

One of the three sequence alignments (see details). Defaults to "all seqs" which is the complete alignment file.

Details

This is a wrapper for the read.dna function from the ape package.

The three MalAvi alignments that can be called are:

• "all seqs" which includes all of the sequences in MalAvi

• "long seqs" which includes only sequences with all or nearly all 479bp

• "morpho seqs" which includes only sequences associated with a morphological species

Value

Each alignment is returned in the form of an object of class DNAbin.

Author(s)

Vincenzo A. Ellis [e-mail]

References

Bensch S, Hellgren O, and Perez-Tris J. 2009. MalAvi: a public database of malaria parasites and related haemosporidians in avian hosts based on mitochondrial cytochrome b lineages. Molecular Ecology Resources 9: 1353-1358. http://mbio-serv2.mbioekol.lu.se/Malavi/

Paradis E., Claude J. & Strimmer K. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289-290.

Examples

## download the "all seqs" alignment
all.seqs <- extract_alignment("all seqs")
all.seqs # take a look

vincenzoaellis/malaviR documentation built on Oct. 10, 2019, 10:55 p.m.