neighbor2<-function(x){
#function to make all 2-neighbors
#x is the input string
out.file<-x #holds result
#First change: 1-neighborhood specification
for(j in 1:6){
for(k in 1:4){
y<-x
if(k!=x[j]){
y[j]<-k
#Second change: becomes 2-neighborhood specification
for(m in 1:6){
if(m!=j){
for(n in 1:4){
z<-y
if(n!=x[m]){
z[m]<-n
out.file<-rbind(out.file,z)
}}}}
}}}
out.file<-out.file[2:length(out.file[,1]),]
return(out.file)
#contains sequence variants with two changes
}