Description Usage Arguments Details Value Author(s) References Examples
View source: R/extract_alignment.R
This function downloads the three sequence alignment files available on the MalAvi website.
1 | extract_alignment(alignment = "all seqs")
|
alignment |
One of the three sequence alignments (see details). Defaults to |
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
Each alignment is returned in the form of an object of class DNAbin
.
Vincenzo A. Ellis vincenzoaellis@gmail.com
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.
1 2 3 | ## download the "all seqs" alignment
all.seqs <- extract_alignment("all seqs")
all.seqs # take a look
|
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