muscle3.7_src
.............\aligngivenpath.cpp
.............\aligngivenpathsw.cpp
.............\aligntwomsas.cpp
.............\aligntwoprofs.cpp
.............\aln.cpp
.............\alpha.cpp
.............\alpha.h
.............\anchors.cpp
.............\bittraceback.cpp
.............\blosum62.cpp
.............\blosumla.cpp
.............\clust.cpp
.............\clust.h
.............\cluster.cpp
.............\cluster.h
.............\clustset.h
.............\clustsetdf.h
.............\clustsetmsa.h
.............\clwwt.cpp
.............\color.cpp
.............\cons.cpp
.............\diaglist.cpp
.............\diaglist.h
.............\diffobjscore.cpp
.............\diffpaths.cpp
.............\difftrees.cpp
.............\difftreese.cpp
.............\distcalc.cpp
.............\distcalc.h
.............\distfunc.cpp
.............\distfunc.h
.............\distpwkimura.cpp
.............\domuscle.cpp
.............\dosp.cpp
.............\dpregionlist.h
.............\dpreglist.cpp
.............\dpreglist.h
.............\drawtree.cpp
.............\edgelist.cpp
.............\edgelist.h
.............\enumopts.cpp
.............\enumopts.h
.............\enums.h
.............\enumtostr.cpp
.............\estring.cpp
.............\estring.h
.............\fasta.cpp
.............\fasta2.cpp
.............\fastclust.cpp
.............\fastdist.cpp
.............\fastdistjones.cpp
.............\fastdistkbit.cpp
.............\fastdistkmer.cpp
.............\fastdistmafft.cpp
.............\fastdistnuc.cpp
.............\fastscorepath2.cpp
.............\finddiags.cpp
.............\finddiagsn.cpp
.............\gapscoredimer.h
.............\glbalign.cpp
.............\glbalign352.cpp
.............\glbaligndiag.cpp
.............\glbalignle.cpp
.............\glbalignsimple.cpp
.............\glbalignsp.cpp
.............\glbalignspn.cpp
.............\glbalignss.cpp
.............\glbalndimer.cpp
.............\globals.cpp
.............\globalslinux.cpp
.............\globalsother.cpp
.............\globalswin32.cpp
.............\gonnet.cpp
.............\gonnet.h
.............\gotowt.cpp
.............\henikoffweight.cpp
.............\henikoffweightpb.cpp
.............\html.cpp
.............\hydro.cpp
.............\intmath.cpp
.............\intmath.h
.............\local.cpp
.............\main.cpp
.............\Makefile
.............\makerootmsa.cpp
.............\makerootmsab.cpp
.............\maketree.cpp
.............\mhack.cpp
.............\mpam200.cpp
.............\msa.cpp
.............\msa.h
.............\msa2.cpp
.............\msadist.h
.............\msadistkimura.cpp
.............\msf.cpp
.............\muscle.cpp
.............\muscle.h
.............\muscleout.cpp
.............\nucmx.cpp