We don't intend it update addss.pl currently. I'd be happy to review a pull request though.

Hi Milot, how do you suggest running addss.pl without the legacy blast, which is not downloadable? Any help would be appreciated.

commented out #"$ncbidir/blastpgp -b 1 -j 1 -h 0.001 -d $dummydb -i $infile -B $tmpfile.in.psi -C $tmpfile.chk 1> $tmpfile.blalog 2> $tmpfile.blalog"

to replace with

"$ncbidir/psiblast -db $dummydb -query $infile -inclusion_ethresh 0.001 -out_pssm $tmpfile.chk -num_iterations 3 -num_alignments 0 1> $tmpfile.blalog 2> $tmpfile.blalog"

and commented out
#&HHPaths::System("$ncbidir/makemat -P $tmpfile");
but unfortunately it is still incapable of adding secondary structure to the alignment.