The aligned file of PR sequences of all patients

This file is generated with a software ClustalX. In this file, the
spaces has been added in a correct way following the alignment. The
file type is phy. I don’t know whether it is in correct format using
github.

If it is, you can try to open file with following codes.

require(Biostrings)
require(seqinr)

virusaln  <- read.alignment(file = "training_data.phy", format =
"phylip")
virusaln$seq