This example is modified from a blog post by Mark Ravinet found at https://genomicislands.wordpress.com/category/r/population-genetics/
#Download ape library from CRAN repository
#install.packages("ape")
#Use library command to make ape functions accessible by this script
library(ape)
#Use paste() function to create a chr vector of accession numbers for Gasterosteus sequences
# These sequences all belong to one genus of sticklebacks
#Change in the tutorial to be sequences previous Endicott
#Bioinformatics students uploaded MT103163-MT103183
seq1 <- paste("JQ", seq(983161, 983255), sep = "") #paste is similar to c(), but output is a string instead of vector
# Download all sequential sequences from Genbank
# This would be really hard to do my hand
# Note that the downloaded sequences are stored in a single variable called a list
sequences <- read.GenBank(seq1,
seq.names = seq1,
species.names = TRUE,
as.character = TRUE)
# Write the sequences to a fasta file
write.dna(sequences, "fish.fasta", format = "fasta")