#' Download MalAvi alignment
#' @importFrom ape read.dna
#' @export
extract_alignment <- function(alignment = "all seqs"){
alignment.names <- c("all seqs", "long seqs", "morpho seqs")
alignment.urls <- c("http://130.235.244.92/Malavi/PHP/get_all_sequences.php",
"http://130.235.244.92/Malavi/PHP/get_long_sequences.php",
"http://130.235.244.92/Malavi/PHP/get_MS_name_sequences_.php")
names(alignment.urls) <- alignment.names
if(!(alignment %in% alignment.names)){
stop('Please choose one of the following alignment names: "all seqs", "long seqs", "morpho seqs"')
} else{
return(read.dna(alignment.urls[alignment], format = "fasta"))
}
}
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