The -stable option had a bug that I was not able to understand or fix. Sometimes incorrect alignments were produced. I don't know how often this happened, but I think it was probably pretty rare because only one user noticed this over a  five year period when thousands of people were using MUSCLE.

I have made a python script stable.py that can be used as a work-around. Usage is:

  python stable.py input.fasta aligned.fasta > stable.fasta

Here, input.fasta is the unaligned sequences used as input to MUSCLE, and aligned.fasta is the output from MUSCLE. The stable.fasta file contains the aligned sequences in the same order as the input file.

Download source code for stable.py.