https://stackoverflow.com/questions/4497747/how-to-perform-basic-multiple-sequence-alignments-in-r?utm_medium=organic&utm_source=google_rich_qa&utm_campaign=google_rich_qa

http://bioconductor.org/packages/release/bioc/html/msa.html provides a few good algorithms for msa.

http://www2.decipher.codes/index.html

Thanks everyone for your suggestions....I will try to work it out

There are multiple ways to do it in R. Go through the stackoverflow discussion and choose the one you find easy to use.

package bio3d , then feed resulting alignment files to MUSCLE web .