Nice questions. Do you need the people here to answer them instead of you? You could get help If you tried something first. Try to answer them and show what you did, then sure people will help you :).

How To Ask Good Questions On Technical And Scientific Forums

This looks a lot like an assignment, and you will learn nothing if someone else solves it for you.

library("gdata")
library("csv")
library(seqinr)
library("Biostrings")
library(msa)
library(ape)

choosebank("genbank")
a1 <- read.GenBank("JF806202", as.character = TRUE)
a1
write.fasta(sequences = a1, names = names(a1), nbchar = 80, file.out = "a.fasta")
a2 <- read.GenBank("JF806212", as.character = TRUE)
a2
write.fasta(sequences = a2, names = names(a2), nbchar = 80, file.out = "b.fasta")
a3 <- read.GenBank("JF806213", as.character = TRUE)
a3
write.fasta(sequences = a3, names = names(a3), nbchar = 80, file.out = "c.fasta")
a4 <- read.GenBank("JF806214", as.character = TRUE)
a4
write.fasta(sequences = a4, names = names(a4), nbchar = 80, file.out = "d.fasta")
a5 <- read.GenBank("JF806215", as.character = TRUE)
a5
write.fasta(sequences = a5, names = names(a5), nbchar = 80, file.out = "e.fasta")
a1=read.fasta(file = "a.fasta")
a2=read.fasta(file = "b.fasta")
a3=read.fasta(file = "c.fasta")
a4=read.fasta(file = "d.fasta")
a5=read.fasta(file = "e.fasta")
a1 <- as.character(a1[[1]])
a2 <- as.character(a2[[1]])
a3 <- as.character(a3[[1]])
a4 <- as.character(a4[[1]])
a5 <- as.character(a5[[1]])
q<-c2s(a1)
q1<-c2s(a2)
q2<-c2s(a3)
q3<-c2s(a5)
q4<-c2s(a5)
q<-toupper(q)
q1<-toupper(q1)
q2<-toupper(q2)
q3<-toupper(q3)
q4<-toupper(q4)

r<- matrix(c(q,q, 1, 1), nrow=1)  
r1<- matrix(c(q1,q1, 1, 1), nrow=1)
r2<- matrix(c(q2,q2, 1, 1), nrow=1)
r3<- matrix(c(q3,q3, 1, 1), nrow=1)
r4<- matrix(c(q4,q4, 1, 1), nrow=1)
data("BLOSUM62")
for (a in r) {

   a<-matrix(score(pairwiseAlignment(r, r1,substitutionMatrix = "BLOSUM62")))
}

This sounds like someone's homework assignment.