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Makefile

aligngivenpath.cpp

aligntwomsas.cpp

aligntwoprofs.cpp

alpha.cpp

alpha.h

anchors.cpp

bittraceback.cpp

debian/README.Debian

debian/changelog

debian/control

debian/copyright

debian/manpage.xml

diffobjscore.cpp

domuscle.cpp

dosp.cpp

dpreglist.cpp

drawtree.cpp

enums.h

estring.cpp

fasta2.cpp

fastdist.cpp

fastdistmafft.cpp

fastdistnuc.cpp

fastscorepath2.cpp

finddiagsn.cpp

glbalign.cpp

glbalign352.cpp

glbaligndiag.cpp

glbalignle.cpp

glbalignsimple.cpp

glbalignspn.cpp

glbalndimer.cpp

globalslinux.cpp

henikoffweight.cpp

local.cpp

main.cpp

makerootmsa.cpp

makerootmsab.cpp

mhack.cpp

mk

msa.cpp

msa.h

msa2.cpp

msadistkimura.cpp

msf.cpp

muscle.cpp

muscle.h

muscleout.cpp

nwdasimple.cpp

nwdasimple2.cpp

nwdasmall.cpp

nwrec.cpp

nwsmall.cpp

objscore.cpp

objscore.h

objscore2.cpp

objscoreda.cpp

options.cpp

outweights.cpp

params.cpp

params.h

phyfromfile.cpp

physeq.cpp

posgap.cpp

ppscore.cpp

profdb.cpp

profile.cpp

profile.h

profilefrommsa.cpp

progalign.cpp

progress.cpp

progressivealign.cpp

readmx.cpp

realigndiffse.cpp

refine.cpp

refinehoriz.cpp

refinetreee.cpp

refinew.cpp

savebest.cpp

scoregaps.cpp

scoremx.cpp

scorepp.cpp

seq.cpp

seqvect.cpp

seqvect.h

stabilize.cpp

subfam.cpp

subfams.cpp

sw.cpp

termgaps.cpp

textfile.cpp

textfile.h

types.h

writescorefile.cpp

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