Nothing
align.muscle <-function(filein, fileout="Sq.fa", gapopen=gapopen, maxiters=maxiters, gapextend=gapextend, call){
read.fasta <- get("read.fasta", pos = "package:seqinr")
strtocall <- paste(call, ' -in ',filein ,' -out',fileout,
'-maxiters',maxiters,'-diags1',
'-gapopen',gapopen)
system(strtocall)
sq<-read.fasta(file=fileout)
sqalineada<-matrix(,length(sq),length(sq[[1]]))
for (i in c(1:length(sq))){
sqalineada[i,]<-sq[[i]]
}
return(sqalineada)
}
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