The following packages will be installed:
 muscle 
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aligngivenpath.cpp
aligngivenpathsw.cpp
aligntwomsas.cpp
aligntwoprofs.cpp
aln.cpp
alpha.cpp
anchors.cpp
bittraceback.cpp
blosum62.cpp
blosumla.cpp
clust.cpp
cluster.cpp
clwwt.cpp
color.cpp
cons.cpp
diaglist.cpp
diffobjscore.cpp
diffpaths.cpp
difftrees.cpp
difftreese.cpp
distcalc.cpp
distfunc.cpp
distpwkimura.cpp
domuscle.cpp
dosp.cpp
dpreglist.cpp
drawtree.cpp
edgelist.cpp
enumopts.cpp
enumtostr.cpp
estring.cpp
fasta2.cpp
fasta.cpp
fastclust.cpp
fastdist.cpp
fastdistjones.cpp
fastdistkbit.cpp
fastdistkmer.cpp
fastdistmafft.cpp
fastdistnuc.cpp
fastscorepath2.cpp
finddiags.cpp
finddiagsn.cpp
glbalign352.cpp
glbalign.cpp
glbaligndiag.cpp
glbalignle.cpp
glbalignsimple.cpp
glbalignsp.cpp
glbalignspn.cpp
glbalignss.cpp
glbalndimer.cpp
globals.cpp
globalslinux.cpp
globalsosx.cpp
globalsother.cpp
globalswin32.cpp
gonnet.cpp
henikoffweight.cpp
henikoffweightpb.cpp
html.cpp
hydro.cpp
intmath.cpp
local.cpp
main.cpp
makerootmsab.cpp
makerootmsa.cpp
maketree.cpp
mhack.cpp
mpam200.cpp
msa2.cpp
msa.cpp
msadistkimura.cpp
msf.cpp
muscle.cpp
muscleout.cpp
nucmx.cpp
nwdasimple2.cpp
nwdasimple.cpp
nwdasmall.cpp
nwrec.cpp
nwsmall.cpp
objscore2.cpp
objscore.cpp
objscoreda.cpp
onexception.cpp
options.cpp
outweights.cpp
pam200mafft.cpp
params.cpp
phy2.cpp
phy3.cpp
phy4.cpp
phy.cpp
phyfromclust.cpp
phyfromfile.cpp
physeq.cpp
phytofile.cpp
posgap.cpp
ppscore.cpp
profdb.cpp
profile.cpp
profilefrommsa.cpp
progalign.cpp
progress.cpp
progressivealign.cpp
pwpath.cpp
readmx.cpp
realigndiffs.cpp
realigndiffse.cpp
refine.cpp
refinehoriz.cpp
refinesubfams.cpp
refinetree.cpp
refinetreee.cpp
refinevert.cpp
refinew.cpp
savebest.cpp
scoredist.cpp
scoregaps.cpp
scorehistory.cpp
scorepp.cpp
seq.cpp
seqvect.cpp
setblosumweights.cpp
setgscweights.cpp
setnewhandler.cpp
spfast.cpp
sptest.cpp
stabilize.cpp
subfam.cpp
subfams.cpp
sw.cpp
termgaps.cpp
textfile.cpp
threewaywt.cpp
tomhydro.cpp
traceback.cpp
tracebackopt.cpp
tracebacksw.cpp
treefrommsa.cpp
typetostr.cpp
upgma2.cpp
usage.cpp
validateids.cpp
vtml2.cpp
writescorefile.cpp
alpha.h
cluster.h
clust.h
clustsetdf.h
clustset.h
clustsetmsa.h
diaglist.h
distcalc.h
distfunc.h
dpregionlist.h
dpreglist.h
edgelist.h
enumopts.h
enums.h
estring.h
gapscoredimer.h
gonnet.h
intmath.h
msadist.h
msadistkimura.h
msadistmafft.h
msa.h
muscle.h
objscore.h
params.h
profile.h
pwpath.h
scorehistory.h
seq.h
seqvect.h
svnversion.h
textfile.h
timing.h
tree.h
types.h
unixio.h
Makefile
stable.py
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  aligngivenpath.cpp -o aligngivenpath.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  aligngivenpathsw.cpp -o aligngivenpathsw.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  aligntwomsas.cpp -o aligntwomsas.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  aligntwoprofs.cpp -o aligntwoprofs.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  aln.cpp -o aln.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  alpha.cpp -o alpha.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  anchors.cpp -o anchors.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  bittraceback.cpp -o bittraceback.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  blosum62.cpp -o blosum62.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  blosumla.cpp -o blosumla.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  clust.cpp -o clust.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  cluster.cpp -o cluster.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  clwwt.cpp -o clwwt.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  color.cpp -o color.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  cons.cpp -o cons.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  diaglist.cpp -o diaglist.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  diffobjscore.cpp -o diffobjscore.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  diffpaths.cpp -o diffpaths.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  difftrees.cpp -o difftrees.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  difftreese.cpp -o difftreese.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  distcalc.cpp -o distcalc.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  distfunc.cpp -o distfunc.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  distpwkimura.cpp -o distpwkimura.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  domuscle.cpp -o domuscle.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  dosp.cpp -o dosp.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  dpreglist.cpp -o dpreglist.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  drawtree.cpp -o drawtree.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  edgelist.cpp -o edgelist.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  enumopts.cpp -o enumopts.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  enumtostr.cpp -o enumtostr.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  estring.cpp -o estring.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  fasta.cpp -o fasta.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  fasta2.cpp -o fasta2.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  fastclust.cpp -o fastclust.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  fastdist.cpp -o fastdist.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  fastdistjones.cpp -o fastdistjones.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  fastdistkbit.cpp -o fastdistkbit.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  fastdistkmer.cpp -o fastdistkmer.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  fastdistmafft.cpp -o fastdistmafft.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  fastdistnuc.cpp -o fastdistnuc.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  fastscorepath2.cpp -o fastscorepath2.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  finddiags.cpp -o finddiags.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  finddiagsn.cpp -o finddiagsn.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  glbalign.cpp -o glbalign.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  glbalign352.cpp -o glbalign352.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  glbaligndiag.cpp -o glbaligndiag.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  glbalignle.cpp -o glbalignle.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  glbalignsimple.cpp -o glbalignsimple.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  glbalignsp.cpp -o glbalignsp.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  glbalignspn.cpp -o glbalignspn.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  glbalignss.cpp -o glbalignss.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  glbalndimer.cpp -o glbalndimer.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  globals.cpp -o globals.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  globalslinux.cpp -o globalslinux.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  globalsosx.cpp -o globalsosx.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  globalsother.cpp -o globalsother.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  globalswin32.cpp -o globalswin32.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  gonnet.cpp -o gonnet.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  henikoffweight.cpp -o henikoffweight.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  henikoffweightpb.cpp -o henikoffweightpb.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  html.cpp -o html.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  hydro.cpp -o hydro.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  intmath.cpp -o intmath.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  local.cpp -o local.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  main.cpp -o main.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  makerootmsa.cpp -o makerootmsa.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  makerootmsab.cpp -o makerootmsab.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  maketree.cpp -o maketree.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  mhack.cpp -o mhack.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  mpam200.cpp -o mpam200.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  msa.cpp -o msa.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  msa2.cpp -o msa2.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  msadistkimura.cpp -o msadistkimura.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  msf.cpp -o msf.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  muscle.cpp -o muscle.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  muscleout.cpp -o muscleout.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  nucmx.cpp -o nucmx.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  nwdasimple.cpp -o nwdasimple.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  nwdasimple2.cpp -o nwdasimple2.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  nwdasmall.cpp -o nwdasmall.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  nwrec.cpp -o nwrec.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  nwsmall.cpp -o nwsmall.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  objscore.cpp -o objscore.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  objscore2.cpp -o objscore2.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  objscoreda.cpp -o objscoreda.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  onexception.cpp -o onexception.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  options.cpp -o options.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  outweights.cpp -o outweights.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  pam200mafft.cpp -o pam200mafft.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  params.cpp -o params.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  phy.cpp -o phy.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  phy2.cpp -o phy2.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  phy3.cpp -o phy3.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  phy4.cpp -o phy4.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  phyfromclust.cpp -o phyfromclust.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  phyfromfile.cpp -o phyfromfile.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  physeq.cpp -o physeq.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  phytofile.cpp -o phytofile.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  posgap.cpp -o posgap.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  ppscore.cpp -o ppscore.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  profdb.cpp -o profdb.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  profile.cpp -o profile.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  profilefrommsa.cpp -o profilefrommsa.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  progalign.cpp -o progalign.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  progress.cpp -o progress.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  progressivealign.cpp -o progressivealign.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  pwpath.cpp -o pwpath.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  readmx.cpp -o readmx.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  realigndiffs.cpp -o realigndiffs.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  realigndiffse.cpp -o realigndiffse.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  refine.cpp -o refine.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  refinehoriz.cpp -o refinehoriz.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  refinesubfams.cpp -o refinesubfams.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  refinetree.cpp -o refinetree.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  refinetreee.cpp -o refinetreee.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  refinevert.cpp -o refinevert.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  refinew.cpp -o refinew.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  savebest.cpp -o savebest.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  scoredist.cpp -o scoredist.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  scoregaps.cpp -o scoregaps.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  scorehistory.cpp -o scorehistory.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  scorepp.cpp -o scorepp.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  seq.cpp -o seq.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  seqvect.cpp -o seqvect.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  setblosumweights.cpp -o setblosumweights.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  setgscweights.cpp -o setgscweights.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  setnewhandler.cpp -o setnewhandler.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  spfast.cpp -o spfast.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  sptest.cpp -o sptest.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  stabilize.cpp -o stabilize.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  subfam.cpp -o subfam.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  subfams.cpp -o subfams.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  sw.cpp -o sw.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  termgaps.cpp -o termgaps.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  textfile.cpp -o textfile.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  threewaywt.cpp -o threewaywt.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  tomhydro.cpp -o tomhydro.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  traceback.cpp -o traceback.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  tracebackopt.cpp -o tracebackopt.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  tracebacksw.cpp -o tracebacksw.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  treefrommsa.cpp -o treefrommsa.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  typetostr.cpp -o typetostr.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  upgma2.cpp -o upgma2.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  usage.cpp -o usage.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  validateids.cpp -o validateids.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  vtml2.cpp -o vtml2.o
g++ -c -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1  writescorefile.cpp -o writescorefile.o
g++ -O2 -march=i586 -mtune=i686 -O3 -funroll-loops -Winline -DNDEBUG=1 -o muscle aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o -lm -static
strip muscle

Slackware package maker, version 3.14159265.

Searching for symbolic links:

No symbolic links were found, so we won't make an installation script.
You can make your own later in ./install/doinst.sh and rebuild the
package if you like.

This next step is optional - you can set the directories in your package
to some sane permissions. If any of the directories in your package have
special permissions, then DO NOT reset them here!

Would you like to reset all directory permissions to 755 (drwxr-xr-x) and
directory ownerships to root.root ([y]es, [n]o)? n

Creating Slackware package:  /usr/src/slapt-src/academic/muscle/muscle-3.8.1551-i586-2salix15.0.txz

./
install/
install/slack-desc
usr/
usr/bin/
usr/bin/muscle
usr/bin/muscle-stable.py
usr/doc/
usr/doc/muscle-3.8.1551/
usr/doc/muscle-3.8.1551/References
usr/doc/muscle-3.8.1551/muscle.SlackBuild
usr/doc/muscle-3.8.1551/muscle_userguide3.8.pdf
usr/man/
usr/man/man1/
usr/man/man1/muscle.1.gz

Slackware package /usr/src/slapt-src/academic/muscle/muscle-3.8.1551-i586-2salix15.0.txz created.

Installing package muscle-3.8.1551-i586-2salix15.0...
| muscle (A multiple sequence alignments program)
| 
| MUSCLE is a program for creating multiple alignments of amino acid
| or nucleotide sequences. A range of options is provided that give
| you the choice of optimizing accuracy, speed, or some compromise
| between the two.
| 
| http://www.drive5.com/muscle/
| http://www.drive5.com/muscle/stable.html
| 
| 
| 
|