This is the tinyest of bugs. The alignment output of
SISSIz --simulate --tstv -n 1 align_in.clustalw > simulated.clustalw
is not loaded by clustal. This is because it does not have the header line:
CLUSTAL W (SISSIz 0.1 simulation)
However running with -v and grep-ing out comments is fine:
SISSIz -v --simulate --tstv -n 1 align_in.clustalw | grep -v "#" > simulated.clustalw
Otherwise, looks great.
Dan Jeffares
WTSI