1. Follow ( https://vlab.amrita.edu/index.php?sub=3&brch=311&sim=1835&cnt=2) to install R in personal computer.
2. Install the SeqinR package.
3. To load “SeqinR” R package follow > library("seqinr")
4. To write a sequence to a FASTA-format file in R, use “write.fasta()”function from the SeqinR R package.
5. Name the output file using the “file.out” argument (input).
6. Read FASTA format file into R using the read.fasta() function from the SeqinR R package.

Example

1. If a user stored DEN-1 Dengue virus sequence in a vector dengueseq, for writing the sequence to a FASTA-format file called “den1.fasta” that contains the sequence labelled as “DEN-1”, follow

   write.fasta(names="DEN-1", sequences=dengueseq, file.out="den1.fasta").

2. To read this FASTA format file follow

   library("seqinr") dengue <- read.fasta(file = "den1.fasta")

3. “den1.fasta” must be saved in the “My Documents” folder of the user’s PC. Procedure to work the simulator

4. A default FASTA file is available on the R platform.

5. User can choose their required sequence and can load the sequence.fasta file into the platform.

   Fig.1. Platform for writing and reading FASTA format in R

6. In case of sequence files other than FASTA file, user have to upload the file and rewrite the name sequence.fasta" into filename.fasta format.

7. Follow the code in the command window: library("seqinr")# This line importing the seqinr library dnaseq<- read.fasta(file = "sequence.fasta") `

8. Click Execute Button for output.