readonly - Revision 19499: /branches/stable/GDE/MUSCLE/src

• ..
• README.txt
• 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
• glbalignla.cpp
• glbalignle.cpp
• glbalignns.cpp
• glbalignsimple.cpp
• glbalignsp.cpp
• glbalignspn.cpp
• glbalignss.cpp
• glbalndimer.cpp
• globals.cpp
• globalslinux.cpp
• globalsosx.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
• makerootmsa.cpp
• makerootmsab.cpp
• maketree.cpp
• mhack.cpp
• mpam200.cpp
• msa.cpp
• msa.h
• msa2.cpp
• msadist.h
• msadistkimura.cpp
• msadistkimura.h
• msadistmafft.h
• msf.cpp
• muscle.cpp
• muscle.h
• muscleout.cpp
• nucmx.cpp
• nwdasimple.cpp
• nwdasimple2.cpp
• nwdasmall.cpp
• nwrec.cpp
• nwsmall.cpp
• objscore.cpp
• objscore.h
• objscore2.cpp
• objscoreda.cpp
• onexception.cpp
• options.cpp
• outweights.cpp
• pam200mafft.cpp
• params.cpp
• params.h
• phy.cpp
• phy2.cpp
• phy3.cpp
• phy4.cpp
• phyfromclust.cpp
• phyfromfile.cpp
• physeq.cpp
• phytofile.cpp
• posgap.cpp
• ppscore.cpp
• profdb.cpp
• profile.cpp
• profile.h
• profilefrommsa.cpp
• progalign.cpp
• progress.cpp
• progressivealign.cpp
• pwpath.cpp
• pwpath.h
• readmx.cpp
• realigndiffs.cpp
• realigndiffse.cpp
• refine.cpp
• refinehoriz.cpp
• refinesubfams.cpp
• refinetree.cpp
• refinetreee.cpp
• refinevert.cpp
• refinew.cpp
• releases.txt
• savebest.cpp
• scoredist.cpp
• scoregaps.cpp
• scorehistory.cpp
• scorehistory.h
• scorepp.cpp
• seq.cpp
• seq.h
• seqvect.cpp
• seqvect.h
• setblosumweights.cpp
• setgscweights.cpp
• setnewhandler.cpp
• spfast.cpp
• sptest.cpp
• stabilize.cpp
• subfam.cpp
• subfams.cpp
• svnmods.h
• svnversion.h
• sw.cpp
• termgaps.cpp
• textfile.cpp
• textfile.h
• threewaywt.cpp
• timing.h
• tomhydro.cpp
• traceback.cpp
• tracebackopt.cpp
• tracebacksw.cpp
• tree.h
• treefrommsa.cpp
• types.h
• typetostr.cpp
• unixio.h
• unused/
• upgma2.cpp
• usage.cpp
• validateids.cpp
• version.txt
• vtml2.cpp
• writescorefile.cpp