I am using a bio3d package from R for sequence alignment. But I am getting some errors while I was running seqaln function, which calls for the installed MUSCLE program. I got the following example from Bio3D tutorial.
pdb <- read.pdb("1bg2") s1 <- aa321(pdb$seqres) s2 <- seq.pdb(pdb) aln <- seqaln( seqbind(s1, s2), id=c("seqres","atom") ) muscle -in C:\Users\Peter \AppData\Local\Temp\RtmpaGTZAD\filee116a23 -out aln.fa - seqtype proteinError in file(file, "r") : cannot open the connection In addition: Warning message: In file(file, "r") : cannot open file 'aln.fa': No such file or directory
I don't understand about this error. your help will be much appreciated.