Converting MultipleAlignments.Rnw to Rmarkdown

[BerylKanali]

@jwokaty Take a look at the changes PDF and HTML for comparison Issues I have:

1. • In the description file when writing authors using this format

Authors@R: c(
  person("Hervé", "Pagès", role=c("aut", "cre"),

is it okay for the first name to be the intials as in the previous format. 2. Graph position not as exact as PDF 3. Size of graph(someone should not scroll to thee the whole graph) 6. The dev.off gives a different output when I knit

null device 
          1 

is the correct output but after in the HTML it shows

## png 
##   2