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simuEvolution <-
function(input,seqL,iLength,nReplicates){
for(reps in 1:nReplicates)
{
nodes<-max(input[,c(1,2)])
OutSeqs<-matrix(ncol=seqL,nrow=nodes)
nt<-c("A","C","T","G")
ancestor<-sample(nt,seqL,replace=TRUE)
OutSeqs[1,]<-ancestor
for(k in 1:nrow(input))
{
f0<-OutSeqs[input[k,1],]
f1<-f0
#substitutions
S1<-round(input[k,3]*length(which(f0!="-")))
mutations<-sample(which(f0!="-"),S1)
for(l in mutations)
f1[l]<-nt[sample(which(f0[l]!=nt),1)]
OutSeqs[input[k,2],]<-f1
#indels
I1<-input[k,4]*length(which(f0!="-"))
i1<-round(I1*input[k,5])
d1<-round(I1*(1-input[k,5]))
#insertions
if(i1>0)
{
mutations2<-sample(which(f0!="-"),(i1))
for(l in mutations2)
#f1[l]<-nt[sample(which(f0[l]!=nt),1)]
{
OutSeqs2<-matrix("-",ncol=(iLength + ncol(OutSeqs)),nrow=nrow(OutSeqs))
OutSeqs2[,c(1:l)]<-OutSeqs[,c(1:l)]
OutSeqs2[,c((l+iLength):ncol(OutSeqs2))]<-OutSeqs[,c(l:ncol(OutSeqs))]
OutSeqs2[k,c((l+1):((l+1)+(iLength-1)))]<-sample(nt,iLength,replace=TRUE)
}
}
#delections
if(d1>0)
{
mutationSites<-length(f0)-iLength
mutations2<-sample(which(f0[1:mutationSites]!="-"),(d1))
for(l in mutations2)
#f1[l]<-nt[sample(which(f0[l]!=nt),1)]
{
OutSeqs2<-OutSeqs
OutSeqs2[k,c((l+1):((l+1)+(iLength-1)))]<-rep("-",iLength)
}
}
OutSeqs<-OutSeqs2
}
gapMAL<-c()
for (l3 in 1:ncol(OutSeqs))
if(paste(OutSeqs[,l3],collapse="")==paste(rep("-",nrow(OutSeqs)),collapse=""))
gapMAL<-c(gapMAL,l3)
if (is.null(gapMAL)==FALSE)
OutSeqsn<-OutSeqs[,-c(gapMAL)] #removes positions full of gaps
for(l2 in 1:nrow(OutSeqs))
write.table(file=paste("simulated_sequences_rep",reps,".fas",sep=""),paste(">",l2,"\n",paste(OutSeqs[l2,],collapse=""),sep=""),col.names=FALSE, row.names=FALSE,quote=FALSE,append=TRUE)
#kk<-read.dna(file="simulated_sequences_rep",reps,".fas",format="fasta")
#dist.dna(kk,model="N")
#plot(nj(dist.dna(kk,model="N")))
tips<-input[which(is.na(match(input[,2],input[,1]))),2]
for(l2 in tips)
write.table(file=paste("simulated_sequences_tips_rep",reps,".fas",sep=""),paste(">",l2,"\n",paste(OutSeqs[l2,],collapse=""),sep=""),col.names=FALSE, row.names=FALSE,quote=FALSE,append=TRUE)
#kk<-read.dna(file="simulated_sequences_tips_rep",reps,".fas",format="fasta")
#dist.dna(kk,model="N")
#plot(nj(dist.dna(kk,model="N")))
}
}
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