muscle3.7_src/aligngivenpath.cpp
muscle3.7_src/aligngivenpathsw.cpp
muscle3.7_src/aligntwomsas.cpp
muscle3.7_src/aligntwoprofs.cpp
muscle3.7_src/aln.cpp
muscle3.7_src/alpha.cpp
muscle3.7_src/alpha.h
muscle3.7_src/anchors.cpp
muscle3.7_src/bittraceback.cpp
muscle3.7_src/blosum62.cpp
muscle3.7_src/blosumla.cpp
muscle3.7_src/clust.cpp
muscle3.7_src/clust.h
muscle3.7_src/cluster.cpp
muscle3.7_src/cluster.h
muscle3.7_src/clustset.h
muscle3.7_src/clustsetdf.h
muscle3.7_src/clustsetmsa.h
muscle3.7_src/clwwt.cpp
muscle3.7_src/color.cpp
muscle3.7_src/cons.cpp
muscle3.7_src/diaglist.cpp
muscle3.7_src/diaglist.h
muscle3.7_src/diffobjscore.cpp
muscle3.7_src/diffpaths.cpp
muscle3.7_src/difftrees.cpp
muscle3.7_src/difftreese.cpp
muscle3.7_src/distcalc.cpp
muscle3.7_src/distcalc.h
muscle3.7_src/distfunc.cpp
muscle3.7_src/distfunc.h
muscle3.7_src/distpwkimura.cpp
muscle3.7_src/domuscle.cpp
muscle3.7_src/dosp.cpp
muscle3.7_src/dpregionlist.h
muscle3.7_src/dpreglist.cpp
muscle3.7_src/dpreglist.h
muscle3.7_src/drawtree.cpp
muscle3.7_src/edgelist.cpp
muscle3.7_src/edgelist.h
muscle3.7_src/enumopts.cpp
muscle3.7_src/enumopts.h
muscle3.7_src/enums.h
muscle3.7_src/enumtostr.cpp
muscle3.7_src/estring.cpp
muscle3.7_src/estring.h
muscle3.7_src/fasta.cpp
muscle3.7_src/fasta2.cpp
muscle3.7_src/fastclust.cpp
muscle3.7_src/fastdist.cpp
muscle3.7_src/fastdistjones.cpp
muscle3.7_src/fastdistkbit.cpp
muscle3.7_src/fastdistkmer.cpp
muscle3.7_src/fastdistmafft.cpp
muscle3.7_src/fastdistnuc.cpp
muscle3.7_src/fastscorepath2.cpp
muscle3.7_src/finddiags.cpp
muscle3.7_src/finddiagsn.cpp
muscle3.7_src/gapscoredimer.h
muscle3.7_src/glbalign.cpp
muscle3.7_src/glbalign352.cpp
muscle3.7_src/glbaligndiag.cpp
muscle3.7_src/glbalignle.cpp
muscle3.7_src/glbalignsimple.cpp
muscle3.7_src/glbalignsp.cpp
muscle3.7_src/glbalignspn.cpp
muscle3.7_src/glbalignss.cpp
muscle3.7_src/glbalndimer.cpp
muscle3.7_src/globals.cpp
muscle3.7_src/globalslinux.cpp
muscle3.7_src/globalsother.cpp
muscle3.7_src/globalswin32.cpp
muscle3.7_src/gonnet.cpp
muscle3.7_src/gonnet.h
muscle3.7_src/gotowt.cpp
muscle3.7_src/henikoffweight.cpp
muscle3.7_src/henikoffweightpb.cpp
muscle3.7_src/html.cpp
muscle3.7_src/hydro.cpp
muscle3.7_src/intmath.cpp
muscle3.7_src/intmath.h
muscle3.7_src/local.cpp
muscle3.7_src/main.cpp
muscle3.7_src/Makefile
muscle3.7_src/makerootmsa.cpp
muscle3.7_src/makerootmsab.cpp
muscle3.7_src/maketree.cpp
muscle3.7_src/mhack.cpp
muscle3.7_src/mpam200.cpp
muscle3.7_src/msa.cpp
muscle3.7_src/msa.h
muscle3.7_src/msa2.cpp
muscle3.7_src/msadist.h
muscle3.7_src/msadistkimura.cpp
muscle3.7_src/msf.cpp
muscle3.7_src/muscle.cpp
muscle3.7_src/muscle.h
muscle3.7_src/muscleout.cpp
muscle3.7_src/nucmx.cpp
muscle3.7_src/nwdasimple.cpp
muscle3.7_src/nwdasimple2.cpp
muscle3.7_src/nwdasmall.cpp
muscle3.7_src/nwrec.cpp
muscle3.7_src/nwsmall.cpp
muscle3.7_src/objscore.cpp
muscle3.7_src/objscore.h
muscle3.7_src/objscore2.cpp
muscle3.7_src/objscoreda.cpp
muscle3.7_src/onexception.cpp
muscle3.7_src/options.cpp
muscle3.7_src/outweights.cpp
muscle3.7_src/pam200mafft.cpp
muscle3.7_src/params.cpp
muscle3.7_src/params.h
muscle3.7_src/phy.cpp
muscle3.7_src/phy2.cpp
muscle3.7_src/phy3.cpp
muscle3.7_src/phy4.cpp
muscle3.7_src/phyfromclust.cpp
muscle3.7_src/phyfromfile.cpp
muscle3.7_src/physeq.cpp
muscle3.7_src/phytofile.cpp
muscle3.7_src/posgap.cpp
muscle3.7_src/ppscore.cpp
muscle3.7_src/profdb.cpp
muscle3.7_src/profile.cpp
muscle3.7_src/profile.h
muscle3.7_src/profilefrommsa.cpp
muscle3.7_src/progalign.cpp
muscle3.7_src/progress.cpp
muscle3.7_src/progressivealign.cpp
muscle3.7_src/pwpath.cpp
muscle3.7_src/pwpath.h
muscle3.7_src/readmx.cpp
muscle3.7_src/realigndiffs.cpp
muscle3.7_src/realigndiffse.cpp
muscle3.7_src/refine.cpp
muscle3.7_src/refinehoriz.cpp
muscle3.7_src/refinesubfams.cpp
muscle3.7_src/refinetree.cpp
muscle3.7_src/refinetreee.cpp
muscle3.7_src/refinevert.cpp
muscle3.7_src/refinew.cpp
muscle3.7_src/savebest.cpp
muscle3.7_src/scoredist.cpp
muscle3.7_src/scoregaps.cpp
muscle3.7_src/scorehistory.cpp
muscle3.7_src/scorehistory.h
muscle3.7_src/scorepp.cpp
muscle3.7_src/seq.cpp
muscle3.7_src/seq.h
muscle3.7_src/seqvect.cpp
muscle3.7_src/seqvect.h
muscle3.7_src/setblosumweights.cpp
muscle3.7_src/setgscweights.cpp
muscle3.7_src/setnewhandler.cpp
muscle3.7_src/spfast.cpp
muscle3.7_src/sptest.cpp
muscle3.7_src/stabilize.cpp
muscle3.7_src/subfam.cpp
muscle3.7_src/subfams.cpp
muscle3.7_src/sw.cpp
muscle3.7_src/termgaps.cpp
muscle3.7_src/textfile.cpp
muscle3.7_src/textfile.h
muscle3.7_src/threewaywt.cpp
muscle3.7_src/timing.h
muscle3.7_src/tomhydro.cpp
muscle3.7_src/traceback.cpp
muscle3.7_src/tracebackopt.cpp
muscle3.7_src/tracebacksw.cpp
muscle3.7_src/tree.h
muscle3.7_src/treefrommsa.cpp
muscle3.7_src/types.h
muscle3.7_src/typetostr.cpp
muscle3.7_src/unixio.h
muscle3.7_src/upgma2.cpp
muscle3.7_src/usage.cpp
muscle3.7_src/validateids.cpp
muscle3.7_src/vtml2.cpp
muscle3.7_src/writescorefile.cpp
muscle3.7_src