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Makefile.am Loading commit data...
Makefile.orig Loading commit data...
aligngivenpath.cpp Loading commit data...
aligngivenpathsw.cpp Loading commit data...
aligntwomsas.cpp Loading commit data...
aligntwoprofs.cpp Loading commit data...
aln.cpp Loading commit data...
alpha.cpp Loading commit data...
alpha.h Loading commit data...
anchoredpp.cpp Loading commit data...
anchors.cpp Loading commit data...
bittraceback.cpp Loading commit data...
blosum62.cpp Loading commit data...
blosumla.cpp Loading commit data...
clust.cpp Loading commit data...
clust.h Loading commit data...
cluster.cpp Loading commit data...
cluster.h Loading commit data...
clustset.h Loading commit data...
clustsetdf.h Loading commit data...
clustsetmsa.h Loading commit data...
clwwt.cpp Loading commit data...
color.cpp Loading commit data...
cons.cpp Loading commit data...
diaglist.cpp Loading commit data...
diaglist.h Loading commit data...
diffobjscore.cpp Loading commit data...
diffpaths.cpp Loading commit data...
difftrees.cpp Loading commit data...
difftreese.cpp Loading commit data...
distcalc.cpp Loading commit data...
distcalc.h Loading commit data...
distfunc.cpp Loading commit data...
distfunc.h Loading commit data...
distpwkimura.cpp Loading commit data...
domuscle.cpp Loading commit data...
dosp.cpp Loading commit data...
dpregionlist.h Loading commit data...
dpreglist.cpp Loading commit data...
dpreglist.h Loading commit data...
drawtree.cpp Loading commit data...
edgelist.cpp Loading commit data...
edgelist.h Loading commit data...
enumopts.cpp Loading commit data...
enumopts.h Loading commit data...
enums.h Loading commit data...
enumtostr.cpp Loading commit data...
estring.cpp Loading commit data...
estring.h Loading commit data...
fasta.cpp Loading commit data...
fasta2.cpp Loading commit data...
fastclust.cpp Loading commit data...
fastdist.cpp Loading commit data...
fastdistjones.cpp Loading commit data...
fastdistkbit.cpp Loading commit data...
fastdistkmer.cpp Loading commit data...
fastdistmafft.cpp Loading commit data...
fastdistnuc.cpp Loading commit data...
fastscorepath2.cpp Loading commit data...
finddiags.cpp Loading commit data...
finddiagsn.cpp Loading commit data...
gapscoredimer.h Loading commit data...
glbalign.cpp Loading commit data...
glbalign352.cpp Loading commit data...
glbaligndiag.cpp Loading commit data...
glbalignle.cpp Loading commit data...
glbalignsimple.cpp Loading commit data...
glbalignsp.cpp Loading commit data...
glbalignspn.cpp Loading commit data...
glbalignss.cpp Loading commit data...
glbalndimer.cpp Loading commit data...
globals.cpp Loading commit data...
globalslinux.cpp Loading commit data...
globalsother.cpp Loading commit data...
globalswin32.cpp Loading commit data...
gonnet.cpp Loading commit data...
gonnet.h Loading commit data...
gotowt.cpp Loading commit data...
henikoffweight.cpp Loading commit data...
henikoffweightpb.cpp Loading commit data...
html.cpp Loading commit data...
hydro.cpp Loading commit data...
intmath.cpp Loading commit data...
intmath.h Loading commit data...
local.cpp Loading commit data...
main.cpp Loading commit data...
makerootmsa.cpp Loading commit data...
makerootmsab.cpp Loading commit data...
maketree.cpp Loading commit data...
mhack.cpp Loading commit data...
mk Loading commit data...
mpam200.cpp Loading commit data...
msa.cpp Loading commit data...
msa.h Loading commit data...
msa2.cpp Loading commit data...
msadist.h Loading commit data...
msadistkimura.cpp Loading commit data...
msf.cpp Loading commit data...
muscle.cpp Loading commit data...
muscle.h Loading commit data...
muscleout.cpp Loading commit data...
nucmx.cpp Loading commit data...
nwdasimple.cpp Loading commit data...
nwdasimple2.cpp Loading commit data...
nwdasmall.cpp Loading commit data...
nwrec.cpp Loading commit data...
nwsmall.cpp Loading commit data...
objscore.cpp Loading commit data...
objscore.h Loading commit data...
objscore2.cpp Loading commit data...
objscoreda.cpp Loading commit data...
onexception.cpp Loading commit data...
options.cpp Loading commit data...
outweights.cpp Loading commit data...
pam200mafft.cpp Loading commit data...
params.cpp Loading commit data...
params.h Loading commit data...
phy.cpp Loading commit data...
phy2.cpp Loading commit data...
phy3.cpp Loading commit data...
phy4.cpp Loading commit data...
phyfromclust.cpp Loading commit data...
phyfromfile.cpp Loading commit data...
physeq.cpp Loading commit data...
phytofile.cpp Loading commit data...
posgap.cpp Loading commit data...
ppscore.cpp Loading commit data...
profdb.cpp Loading commit data...
profile.cpp Loading commit data...
profile.h Loading commit data...
profilefrommsa.cpp Loading commit data...
profout.musc Loading commit data...
progalign.cpp Loading commit data...
progress.cpp Loading commit data...
progressivealign.cpp Loading commit data...
pwpath.cpp Loading commit data...
pwpath.h Loading commit data...
readmx.cpp Loading commit data...
realigndiffs.cpp Loading commit data...
realigndiffse.cpp Loading commit data...
refine.cpp Loading commit data...
refine.h Loading commit data...
refinehoriz.cpp Loading commit data...
refinesubfams.cpp Loading commit data...
refinetree.cpp Loading commit data...
refinetreee.cpp Loading commit data...
refinevert.cpp Loading commit data...
refinew.cpp Loading commit data...
savebest.cpp Loading commit data...
scoredist.cpp Loading commit data...
scoregaps.cpp Loading commit data...
scorehistory.cpp Loading commit data...
scorehistory.h Loading commit data...
scorepp.cpp Loading commit data...
seq.cpp Loading commit data...
seq.h Loading commit data...
seqvect.cpp Loading commit data...
seqvect.h Loading commit data...
setblosumweights.cpp Loading commit data...
setgscweights.cpp Loading commit data...
setnewhandler.cpp Loading commit data...
spfast.cpp Loading commit data...
sptest.cpp Loading commit data...
stabilize.cpp Loading commit data...
subfam.cpp Loading commit data...
subfams.cpp Loading commit data...
sw.cpp Loading commit data...
termgaps.cpp Loading commit data...
test.musc Loading commit data...
test.out Loading commit data...
test.prof Loading commit data...
textfile.cpp Loading commit data...
textfile.h Loading commit data...
threadstorage.h Loading commit data...
threewaywt.cpp Loading commit data...
timing.h Loading commit data...
tomhydro.cpp Loading commit data...
traceback.cpp Loading commit data...
tracebackopt.cpp Loading commit data...
tracebacksw.cpp Loading commit data...
tree.h Loading commit data...
treefrommsa.cpp Loading commit data...
types.h Loading commit data...
typetostr.cpp Loading commit data...
unixio.h Loading commit data...
upgma2.cpp Loading commit data...
usage.cpp Loading commit data...
validateids.cpp Loading commit data...
vtml2.cpp Loading commit data...
writescorefile.cpp Loading commit data...