Muscle seqaln( ) in linux vs Windows? (2)

I used seqaln() in Windows. I had no problem. But when I used it with the same proteins in linux, seqaln() returns different and wrong results.

I have a list of proteins. In a for loop i execute read.fasta() for each protein and seqaln() with a pdb fasta sequence corresponding to each protein. I had no issue in Windows. But, in linux seqaln() is done with the previous protein fasta not the current one.