runGubbins <- function(fastaCore, prefix, gargs='--threads 4 -t fasttree'){
if (Sys.which('run_gubbins.py')==''){
stop('"run_gubbins.py" in not in your $PATH.')
}
gargs <- paste0(gargs,' -p ', prefix)
gubbins <- paste('run_gubbins.py', gargs, fastaCore)
system(gubbins)
out <- c()
out[1] <- paste0(prefix, '.branch_base_reconstruction.embl')
out[2] <- paste0(prefix, '.recombination_predictions.gff')
out[3] <- paste0(prefix, '.recombination_predictions.embl')
out[4] <- paste0(prefix, '.filtered_polymorphic_sites.phylip')
out[5] <- paste0(prefix, '.summary_of_snp_distribution.vcf')
out[6] <- paste0(prefix, '.per_branch_statistics.csv')
out[7] <- paste0(prefix, '.filtered_polymorphic_sites.fasta')
out[8] <- paste0(prefix, '.node_labelled.final_tree.tre')
out[9] <- paste0(prefix, '.final_tree.tre')
return(out)
}
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