library(msa) hemoURL <- "http://www.bioinf.jku.at/software/msa/HemoglobinExample.fasta" mySeqs <- readAAStringSet(hemoURL) res <- msaClustalW(mySeqs) msaPrettyPrint(x=res, file="HemoglobinExample.pdf", paperWidth=15.3, paperHeight=4.5, shadingMode="functional", shadingModeArg="structure", shadingColors="greens", logoColors="rasmol", showLogoScale="right", showLegend=FALSE, askForOverwrite=FALSE) ## white space around the resulting plot can be removed using the tool pdfcrop ## system("pdfcrop HemoglobinExample.pdf")