Tree @bbeb9724-7c46-4983-88d4-5c78c839af34/upstream/3.7+4565 (Download .tar.gz)
- ..
- aligngivenpath.cpp
- aligngivenpathsw.cpp
- aligntwomsas.cpp
- aligntwoprofs.cpp
- aln.cpp
- alpha.cpp
- alpha.h
- anchoredpp.cpp
- 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.am
- Makefile.orig
- makerootmsa.cpp
- makerootmsab.cpp
- maketree.cpp
- mhack.cpp
- mk
- mpam200.cpp
- msa.cpp
- msa.h
- msa2.cpp
- msadist.h
- msadistkimura.cpp
- 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
- profout.musc
- progalign.cpp
- progress.cpp
- progressivealign.cpp
- pwpath.cpp
- pwpath.h
- readmx.cpp
- realigndiffs.cpp
- realigndiffse.cpp
- refine.cpp
- refine.h
- refinehoriz.cpp
- refinesubfams.cpp
- refinetree.cpp
- refinetreee.cpp
- refinevert.cpp
- refinew.cpp
- 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
- sw.cpp
- termgaps.cpp
- test.musc
- test.out
- test.prof
- textfile.cpp
- textfile.h
- threadstorage.h
- threewaywt.cpp
- timing.h
- tomhydro.cpp
- traceback.cpp
- tracebackopt.cpp
- tracebacksw.cpp
- tree.h
- treefrommsa.cpp
- types.h
- typetostr.cpp
- unixio.h
- upgma2.cpp
- usage.cpp
- validateids.cpp
- vtml2.cpp
- writescorefile.cpp