From 085a5ff2a7701ffecdd38a6b398f4e0bc652d6a9 Mon Sep 17 00:00:00 2001
From: alain viari <alain.viari@inria.fr>
Date: Sat, 14 Nov 2015 00:11:27 +0100
Subject: [PATCH] squared muscle

Former-commit-id: 54638fc7623ec0485109b0b5879144f8f2514213
Former-commit-id: 23f43cd31169d95df12ae1c207d9fd1c924d26b1
---
 config/default.conf                           |  10 +++---
 config/targets/lxbin.targ                     |   2 +-
 config/targets/package.targ                   |   1 -
 src/hmmer3/Makefile                           |   4 ---
 src/kimono/Makefile                           |   6 ----
 src/muscle/Makefile                           |   6 ----
 src/muscle/muscle3.8.31/Makefile              |  31 ++++++++----------
 src/muscle/muscle3.8.31/{src => }/README.txt  |   0
 .../muscle3.8.31/{src => }/aligngivenpath.cpp |   0
 .../{src => }/aligngivenpathsw.cpp            |   0
 .../muscle3.8.31/{src => }/aligntwomsas.cpp   |   0
 .../muscle3.8.31/{src => }/aligntwoprofs.cpp  |   0
 src/muscle/muscle3.8.31/{src => }/aln.cpp     |   0
 src/muscle/muscle3.8.31/{src => }/alpha.cpp   |   0
 src/muscle/muscle3.8.31/{src => }/alpha.h     |   0
 src/muscle/muscle3.8.31/{src => }/anchors.cpp |   0
 .../muscle3.8.31/{src => }/bittraceback.cpp   |   0
 .../muscle3.8.31/{src => }/blosum62.cpp       |   0
 .../muscle3.8.31/{src => }/blosumla.cpp       |   0
 src/muscle/muscle3.8.31/{src => }/clust.cpp   |   0
 src/muscle/muscle3.8.31/{src => }/clust.h     |   0
 src/muscle/muscle3.8.31/{src => }/cluster.cpp |   0
 src/muscle/muscle3.8.31/{src => }/cluster.h   |   0
 src/muscle/muscle3.8.31/{src => }/clustset.h  |   0
 .../muscle3.8.31/{src => }/clustsetdf.h       |   0
 .../muscle3.8.31/{src => }/clustsetmsa.h      |   0
 src/muscle/muscle3.8.31/{src => }/clwwt.cpp   |   0
 src/muscle/muscle3.8.31/{src => }/color.cpp   |   0
 src/muscle/muscle3.8.31/{src => }/cons.cpp    |   0
 .../muscle3.8.31/{src => }/diaglist.cpp       |   0
 src/muscle/muscle3.8.31/{src => }/diaglist.h  |   0
 .../muscle3.8.31/{src => }/diffobjscore.cpp   |   0
 .../muscle3.8.31/{src => }/diffpaths.cpp      |   0
 .../muscle3.8.31/{src => }/difftrees.cpp      |   0
 .../muscle3.8.31/{src => }/difftreese.cpp     |   0
 .../muscle3.8.31/{src => }/distcalc.cpp       |   0
 src/muscle/muscle3.8.31/{src => }/distcalc.h  |   0
 .../muscle3.8.31/{src => }/distfunc.cpp       |   0
 src/muscle/muscle3.8.31/{src => }/distfunc.h  |   0
 .../muscle3.8.31/{src => }/distpwkimura.cpp   |   0
 .../muscle3.8.31/{src => }/domuscle.cpp       |   0
 src/muscle/muscle3.8.31/{src => }/dosp.cpp    |   0
 .../muscle3.8.31/{src => }/dpregionlist.h     |   0
 .../muscle3.8.31/{src => }/dpreglist.cpp      |   0
 src/muscle/muscle3.8.31/{src => }/dpreglist.h |   0
 .../muscle3.8.31/{src => }/drawtree.cpp       |   0
 .../muscle3.8.31/{src => }/edgelist.cpp       |   0
 src/muscle/muscle3.8.31/{src => }/edgelist.h  |   0
 .../muscle3.8.31/{src => }/enumopts.cpp       |   0
 src/muscle/muscle3.8.31/{src => }/enumopts.h  |   0
 src/muscle/muscle3.8.31/{src => }/enums.h     |   0
 .../muscle3.8.31/{src => }/enumtostr.cpp      |   0
 src/muscle/muscle3.8.31/{src => }/estring.cpp |   0
 src/muscle/muscle3.8.31/{src => }/estring.h   |   0
 src/muscle/muscle3.8.31/{src => }/fasta.cpp   |   0
 src/muscle/muscle3.8.31/{src => }/fasta2.cpp  |   0
 .../muscle3.8.31/{src => }/fastclust.cpp      |   0
 .../muscle3.8.31/{src => }/fastdist.cpp       |   0
 .../muscle3.8.31/{src => }/fastdistjones.cpp  |   0
 .../muscle3.8.31/{src => }/fastdistkbit.cpp   |   0
 .../muscle3.8.31/{src => }/fastdistkmer.cpp   |   0
 .../muscle3.8.31/{src => }/fastdistmafft.cpp  |   0
 .../muscle3.8.31/{src => }/fastdistnuc.cpp    |   0
 .../muscle3.8.31/{src => }/fastscorepath2.cpp |   0
 .../muscle3.8.31/{src => }/finddiags.cpp      |   0
 .../muscle3.8.31/{src => }/finddiagsn.cpp     |   0
 .../muscle3.8.31/{src => }/gapscoredimer.h    |   0
 src/muscle/muscle3.8.31/{src => }/gatest.cpp  |   0
 .../muscle3.8.31/{src => }/glbalign.cpp       |   0
 .../muscle3.8.31/{src => }/glbalign352.cpp    |   0
 .../muscle3.8.31/{src => }/glbaligndiag.cpp   |   0
 .../muscle3.8.31/{src => }/glbalignla.cpp     |   0
 .../muscle3.8.31/{src => }/glbalignle.cpp     |   0
 .../muscle3.8.31/{src => }/glbalignns.cpp     |   0
 .../muscle3.8.31/{src => }/glbalignsimple.cpp |   0
 .../muscle3.8.31/{src => }/glbalignsp.cpp     |   0
 .../muscle3.8.31/{src => }/glbalignspn.cpp    |   0
 .../muscle3.8.31/{src => }/glbalignss.cpp     |   0
 .../muscle3.8.31/{src => }/glbalndimer.cpp    |   0
 src/muscle/muscle3.8.31/{src => }/globals.cpp |   0
 .../muscle3.8.31/{src => }/globalslinux.cpp   |   0
 .../muscle3.8.31/{src => }/globalsosx.cpp     |   0
 .../muscle3.8.31/{src => }/globalsother.cpp   |   0
 .../muscle3.8.31/{src => }/globalswin32.cpp   |   0
 src/muscle/muscle3.8.31/{src => }/gonnet.cpp  |   0
 src/muscle/muscle3.8.31/{src => }/gonnet.h    |   0
 src/muscle/muscle3.8.31/{src => }/gotowt.cpp  |   0
 .../muscle3.8.31/{src => }/henikoffweight.cpp |   0
 .../{src => }/henikoffweightpb.cpp            |   0
 src/muscle/muscle3.8.31/{src => }/html.cpp    |   0
 src/muscle/muscle3.8.31/{src => }/hydro.cpp   |   0
 src/muscle/muscle3.8.31/{src => }/intmath.cpp |   0
 src/muscle/muscle3.8.31/{src => }/intmath.h   |   0
 src/muscle/muscle3.8.31/{src => }/local.cpp   |   0
 src/muscle/muscle3.8.31/{src => }/main.cpp    |   0
 src/muscle/muscle3.8.31/{src => }/make.err    |   0
 src/muscle/muscle3.8.31/{src => }/make.out    |   0
 .../muscle3.8.31/{src => }/makerootmsa.cpp    |   0
 .../muscle3.8.31/{src => }/makerootmsab.cpp   |   0
 .../muscle3.8.31/{src => }/maketree.cpp       |   0
 src/muscle/muscle3.8.31/{src => }/mhack.cpp   |   0
 src/muscle/muscle3.8.31/{src => }/mk          |   0
 src/muscle/muscle3.8.31/{src => }/mpam200.cpp |   0
 src/muscle/muscle3.8.31/{src => }/msa.cpp     |   0
 src/muscle/muscle3.8.31/{src => }/msa.h       |   0
 src/muscle/muscle3.8.31/{src => }/msa2.cpp    |   0
 src/muscle/muscle3.8.31/{src => }/msadist.h   |   0
 .../muscle3.8.31/{src => }/msadistkimura.cpp  |   0
 .../muscle3.8.31/{src => }/msadistkimura.h    |   0
 .../muscle3.8.31/{src => }/msadistmafft.h     |   0
 src/muscle/muscle3.8.31/{src => }/msf.cpp     |   0
 src/muscle/muscle3.8.31/{src => }/muscle.cpp  |   0
 src/muscle/muscle3.8.31/{src => }/muscle.h    |   0
 .../muscle3.8.31/muscle.make.stderr.txt       |   0
 .../muscle3.8.31/muscle.make.stdout.txt       |   0
 .../muscle3.8.31/{src => }/muscle.vcproj      |   0
 src/muscle/muscle3.8.31/{src => }/muscle21    | Bin
 .../muscle3.8.31/{src => }/muscle21.vcproj    |   0
 .../muscle3.8.31/{src => }/muscleout.cpp      |   0
 src/muscle/muscle3.8.31/{src => }/nucmx.cpp   |   0
 .../muscle3.8.31/{src => }/nwdasimple.cpp     |   0
 .../muscle3.8.31/{src => }/nwdasimple2.cpp    |   0
 .../muscle3.8.31/{src => }/nwdasmall.cpp      |   0
 src/muscle/muscle3.8.31/{src => }/nwrec.cpp   |   0
 src/muscle/muscle3.8.31/{src => }/nwsmall.cpp |   0
 .../muscle3.8.31/{src => }/objscore.cpp       |   0
 src/muscle/muscle3.8.31/{src => }/objscore.h  |   0
 .../muscle3.8.31/{src => }/objscore2.cpp      |   0
 .../muscle3.8.31/{src => }/objscoreda.cpp     |   0
 .../muscle3.8.31/{src => }/onexception.cpp    |   0
 src/muscle/muscle3.8.31/{src => }/options.cpp |   0
 .../muscle3.8.31/{src => }/outweights.cpp     |   0
 .../muscle3.8.31/{src => }/pam200mafft.cpp    |   0
 src/muscle/muscle3.8.31/{src => }/params.cpp  |   0
 src/muscle/muscle3.8.31/{src => }/params.h    |   0
 src/muscle/muscle3.8.31/{src => }/phy.cpp     |   0
 src/muscle/muscle3.8.31/{src => }/phy2.cpp    |   0
 src/muscle/muscle3.8.31/{src => }/phy3.cpp    |   0
 src/muscle/muscle3.8.31/{src => }/phy4.cpp    |   0
 .../muscle3.8.31/{src => }/phyfromclust.cpp   |   0
 .../muscle3.8.31/{src => }/phyfromfile.cpp    |   0
 src/muscle/muscle3.8.31/{src => }/physeq.cpp  |   0
 .../muscle3.8.31/{src => }/phytofile.cpp      |   0
 src/muscle/muscle3.8.31/{src => }/posgap.cpp  |   0
 src/muscle/muscle3.8.31/{src => }/ppscore.cpp |   0
 src/muscle/muscle3.8.31/{src => }/profdb.cpp  |   0
 src/muscle/muscle3.8.31/{src => }/profile.cpp |   0
 src/muscle/muscle3.8.31/{src => }/profile.h   |   0
 .../muscle3.8.31/{src => }/profilefrommsa.cpp |   0
 .../muscle3.8.31/{src => }/progalign.cpp      |   0
 .../muscle3.8.31/{src => }/progress.cpp       |   0
 .../{src => }/progressivealign.cpp            |   0
 src/muscle/muscle3.8.31/{src => }/pwpath.cpp  |   0
 src/muscle/muscle3.8.31/{src => }/pwpath.h    |   0
 src/muscle/muscle3.8.31/{src => }/readmx.cpp  |   0
 .../muscle3.8.31/{src => }/realigndiffs.cpp   |   0
 .../muscle3.8.31/{src => }/realigndiffse.cpp  |   0
 .../muscle3.8.31/{src => }/redblack.cpp       |   0
 src/muscle/muscle3.8.31/{src => }/refine.cpp  |   0
 .../muscle3.8.31/{src => }/refinehoriz.cpp    |   0
 .../muscle3.8.31/{src => }/refinesubfams.cpp  |   0
 .../muscle3.8.31/{src => }/refinetree.cpp     |   0
 .../muscle3.8.31/{src => }/refinetreee.cpp    |   0
 .../muscle3.8.31/{src => }/refinevert.cpp     |   0
 src/muscle/muscle3.8.31/{src => }/refinew.cpp |   0
 .../muscle3.8.31/{src => }/releases.txt       |   0
 .../muscle3.8.31/{src => }/savebest.cpp       |   0
 .../muscle3.8.31/{src => }/scoredist.cpp      |   0
 .../muscle3.8.31/{src => }/scoregaps.cpp      |   0
 .../muscle3.8.31/{src => }/scorehistory.cpp   |   0
 .../muscle3.8.31/{src => }/scorehistory.h     |   0
 src/muscle/muscle3.8.31/{src => }/scoremx.cpp |   0
 src/muscle/muscle3.8.31/{src => }/scorepp.cpp |   0
 src/muscle/muscle3.8.31/{src => }/seq.cpp     |   0
 src/muscle/muscle3.8.31/{src => }/seq.h       |   0
 src/muscle/muscle3.8.31/{src => }/seqvect.cpp |   0
 src/muscle/muscle3.8.31/{src => }/seqvect.h   |   0
 .../{src => }/setblosumweights.cpp            |   0
 .../muscle3.8.31/{src => }/setgscweights.cpp  |   0
 .../muscle3.8.31/{src => }/setnewhandler.cpp  |   0
 src/muscle/muscle3.8.31/{src => }/spfast.cpp  |   0
 src/muscle/muscle3.8.31/{src => }/sptest.cpp  |   0
 src/muscle/muscle3.8.31/src/Makefile          |  11 -------
 .../muscle3.8.31/{src => }/stabilize.cpp      |   0
 src/muscle/muscle3.8.31/{src => }/subfam.cpp  |   0
 src/muscle/muscle3.8.31/{src => }/subfams.cpp |   0
 src/muscle/muscle3.8.31/{src => }/svnmods.h   |   0
 .../muscle3.8.31/{src => }/svnversion.h       |   0
 src/muscle/muscle3.8.31/{src => }/sw.cpp      |   0
 .../muscle3.8.31/{src => }/termgaps.cpp       |   0
 .../muscle3.8.31/{src => }/textfile.cpp       |   0
 src/muscle/muscle3.8.31/{src => }/textfile.h  |   0
 .../muscle3.8.31/{src => }/threewaywt.cpp     |   0
 src/muscle/muscle3.8.31/{src => }/timing.h    |   0
 .../muscle3.8.31/{src => }/tomhydro.cpp       |   0
 .../muscle3.8.31/{src => }/traceback.cpp      |   0
 .../muscle3.8.31/{src => }/tracebackopt.cpp   |   0
 .../muscle3.8.31/{src => }/tracebacksw.cpp    |   0
 src/muscle/muscle3.8.31/{src => }/tree.h      |   0
 .../muscle3.8.31/{src => }/treefrommsa.cpp    |   0
 src/muscle/muscle3.8.31/{src => }/types.h     |   0
 .../muscle3.8.31/{src => }/typetostr.cpp      |   0
 src/muscle/muscle3.8.31/{src => }/unixio.h    |   0
 src/muscle/muscle3.8.31/{src => }/upgma2.cpp  |   0
 src/muscle/muscle3.8.31/{src => }/usage.cpp   |   0
 .../muscle3.8.31/{src => }/validateids.cpp    |   0
 src/muscle/muscle3.8.31/{src => }/version.txt |   0
 src/muscle/muscle3.8.31/{src => }/vtml2.cpp   |   0
 .../muscle3.8.31/{src => }/writescorefile.cpp |   0
 src/prokov/Makefile                           |   3 --
 210 files changed, 20 insertions(+), 54 deletions(-)
 rename src/muscle/muscle3.8.31/{src => }/README.txt (100%)
 rename src/muscle/muscle3.8.31/{src => }/aligngivenpath.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/aligngivenpathsw.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/aligntwomsas.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/aligntwoprofs.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/aln.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/alpha.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/alpha.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/anchors.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/bittraceback.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/blosum62.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/blosumla.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/clust.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/clust.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/cluster.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/cluster.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/clustset.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/clustsetdf.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/clustsetmsa.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/clwwt.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/color.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/cons.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/diaglist.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/diaglist.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/diffobjscore.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/diffpaths.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/difftrees.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/difftreese.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/distcalc.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/distcalc.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/distfunc.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/distfunc.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/distpwkimura.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/domuscle.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/dosp.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/dpregionlist.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/dpreglist.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/dpreglist.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/drawtree.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/edgelist.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/edgelist.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/enumopts.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/enumopts.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/enums.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/enumtostr.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/estring.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/estring.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/fasta.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/fasta2.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/fastclust.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/fastdist.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/fastdistjones.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/fastdistkbit.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/fastdistkmer.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/fastdistmafft.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/fastdistnuc.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/fastscorepath2.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/finddiags.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/finddiagsn.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/gapscoredimer.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/gatest.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/glbalign.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/glbalign352.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/glbaligndiag.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/glbalignla.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/glbalignle.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/glbalignns.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/glbalignsimple.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/glbalignsp.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/glbalignspn.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/glbalignss.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/glbalndimer.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/globals.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/globalslinux.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/globalsosx.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/globalsother.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/globalswin32.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/gonnet.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/gonnet.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/gotowt.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/henikoffweight.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/henikoffweightpb.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/html.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/hydro.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/intmath.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/intmath.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/local.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/main.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/make.err (100%)
 rename src/muscle/muscle3.8.31/{src => }/make.out (100%)
 rename src/muscle/muscle3.8.31/{src => }/makerootmsa.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/makerootmsab.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/maketree.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/mhack.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/mk (100%)
 rename src/muscle/muscle3.8.31/{src => }/mpam200.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/msa.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/msa.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/msa2.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/msadist.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/msadistkimura.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/msadistkimura.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/msadistmafft.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/msf.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/muscle.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/muscle.h (100%)
 create mode 100644 src/muscle/muscle3.8.31/muscle.make.stderr.txt
 create mode 100644 src/muscle/muscle3.8.31/muscle.make.stdout.txt
 rename src/muscle/muscle3.8.31/{src => }/muscle.vcproj (100%)
 rename src/muscle/muscle3.8.31/{src => }/muscle21 (100%)
 rename src/muscle/muscle3.8.31/{src => }/muscle21.vcproj (100%)
 rename src/muscle/muscle3.8.31/{src => }/muscleout.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/nucmx.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/nwdasimple.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/nwdasimple2.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/nwdasmall.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/nwrec.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/nwsmall.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/objscore.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/objscore.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/objscore2.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/objscoreda.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/onexception.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/options.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/outweights.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/pam200mafft.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/params.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/params.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/phy.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/phy2.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/phy3.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/phy4.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/phyfromclust.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/phyfromfile.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/physeq.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/phytofile.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/posgap.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/ppscore.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/profdb.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/profile.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/profile.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/profilefrommsa.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/progalign.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/progress.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/progressivealign.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/pwpath.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/pwpath.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/readmx.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/realigndiffs.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/realigndiffse.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/redblack.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/refine.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/refinehoriz.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/refinesubfams.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/refinetree.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/refinetreee.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/refinevert.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/refinew.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/releases.txt (100%)
 rename src/muscle/muscle3.8.31/{src => }/savebest.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/scoredist.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/scoregaps.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/scorehistory.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/scorehistory.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/scoremx.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/scorepp.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/seq.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/seq.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/seqvect.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/seqvect.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/setblosumweights.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/setgscweights.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/setnewhandler.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/spfast.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/sptest.cpp (100%)
 delete mode 100644 src/muscle/muscle3.8.31/src/Makefile
 rename src/muscle/muscle3.8.31/{src => }/stabilize.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/subfam.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/subfams.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/svnmods.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/svnversion.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/sw.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/termgaps.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/textfile.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/textfile.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/threewaywt.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/timing.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/tomhydro.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/traceback.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/tracebackopt.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/tracebacksw.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/tree.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/treefrommsa.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/types.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/typetostr.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/unixio.h (100%)
 rename src/muscle/muscle3.8.31/{src => }/upgma2.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/usage.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/validateids.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/version.txt (100%)
 rename src/muscle/muscle3.8.31/{src => }/vtml2.cpp (100%)
 rename src/muscle/muscle3.8.31/{src => }/writescorefile.cpp (100%)

diff --git a/config/default.conf b/config/default.conf
index 8bdb54c..566a765 100644
--- a/config/default.conf
+++ b/config/default.conf
@@ -118,10 +118,12 @@ INCDIR	 =	$(abspath $(PRTDIR))/include
 # default gmake variable in implicit rules
 # ------------------------------------
 
-CFLAGS 	  := $(CFLAGS)	$(OPTIM) $(MACHDEF) -I$(INCDIR)
+#CFLAGS 	  := $(CFLAGS) $(OPTIM) $(MACHDEF) -I$(INCDIR)
+CFLAGS 	  = $(OPTIM) $(MACHDEF) -I$(INCDIR)
 
-LDFLAGS	  := $(LDFLAGS)    -L$(LIBDIR) -L.
+#LDFLAGS	  := $(LDFLAGS) -L$(LIBDIR) -L.
+LDFLAGS	  = -L$(LIBDIR) -L.
 
-LDLIBS	  =	    $(LIBS) $(MALLOC_LIBS) $(MATH_LIBS) $(CC_LIBS)
+LDLIBS	  =	$(LIBS) $(MALLOC_LIBS) $(MATH_LIBS) $(CC_LIBS)
 
-LINTFLAGS = 	$(MACHDEF) -I$(INCDIR)
+LINTFLAGS = $(MACHDEF) -I$(INCDIR)
diff --git a/config/targets/lxbin.targ b/config/targets/lxbin.targ
index 4e6dbe9..f8063f5 100644
--- a/config/targets/lxbin.targ
+++ b/config/targets/lxbin.targ
@@ -34,7 +34,7 @@ all::	prelib $(PROGS) install
 
 prelib::
 	test -d $(PRTDIR) || mkdir $(PRTDIR)  # because some linker may complain
-	test -d $(LIBDIR) || mkdir $(LIBDIR)  # if -L$(LIBDIR) does not exist
+	test -d $(LIBDIR) || mkdir $(LIBDIR)  # if LIBDIR does not exist
 
 install::
 	test -d $(PRTDIR) || mkdir $(PRTDIR)
diff --git a/config/targets/package.targ b/config/targets/package.targ
index 40550dc..55733de 100644
--- a/config/targets/package.targ
+++ b/config/targets/package.targ
@@ -31,7 +31,6 @@ pkg.expand::
 	test -f $(PKGDIR)/configure || $(TAR) zxf $(PKGTAR) -C $(PKGDIR) --strip-components 1
 
 pkg.make:: pkg.expand
-	echo $(PKG_CONFIG)
 	test -f $(PKGDIR)/Makefile || (export PATH="$(PRTPATH_BIN):$$PATH" && \
 	                               export PKG_CONFIG=$(PKG_CONFIG) && \
 	                               export CC="$(CC)" && \
diff --git a/src/hmmer3/Makefile b/src/hmmer3/Makefile
index 977c199..b101e2f 100644
--- a/src/hmmer3/Makefile
+++ b/src/hmmer3/Makefile
@@ -22,7 +22,3 @@ include $(CFGDIR)targets/package.targ
 
 include $(CFGDIR)targets/help.targ
 
-# bug fix
-all::
-	-mkdir $(PKGDIR)/userguide
-
diff --git a/src/kimono/Makefile b/src/kimono/Makefile
index c9e9752..7aec888 100755
--- a/src/kimono/Makefile
+++ b/src/kimono/Makefile
@@ -22,9 +22,3 @@ DIRS = lxpack
 include ../../config/targets/propagate.targ
 
 include ../../config/targets/help.targ
-
-all::
-	$(MAKE) ACTION=$@ _action
-
-clean::
-	$(MAKE) -C lxpack portclean
diff --git a/src/muscle/Makefile b/src/muscle/Makefile
index 6e300a0..d0fb99f 100755
--- a/src/muscle/Makefile
+++ b/src/muscle/Makefile
@@ -22,9 +22,3 @@ DIRS = muscle3.8.31
 include ../../config/targets/propagate.targ
 
 include ../../config/targets/help.targ
-
-all::
-	$(MAKE) ACTION=$@ _action
-
-clean::
-	$(MAKE) -C lxpack portclean
diff --git a/src/muscle/muscle3.8.31/Makefile b/src/muscle/muscle3.8.31/Makefile
index d16c191..c9841e9 100755
--- a/src/muscle/muscle3.8.31/Makefile
+++ b/src/muscle/muscle3.8.31/Makefile
@@ -2,29 +2,24 @@
 # $Id: $
 # ---------------------------------------------------------------
 # @file: Makefile
-# @desc: makefile for lxpack
-#
-# @history:
-# @history:
-# @+	    <Gloup> : Apr 97 : Created
-# @+	    <Gloup> : Mar 02 : Updated for LXxware
-#
-# @note: should be processed with gnu compatible make
-# @note: helixware_compatible
-#
-# @end:
+# @desc: makefile for muscle
 # ---------------------------------------------------------------
 #
 include ../../../config/auto.conf
 
-DIRS = src
+all: muscle install 
 
-include ../../../config/targets/propagate.targ
+muscle:
+	chmod +x ./mk
+	(export CXX=$(CXX) && ./mk)
 
-include ../../../config/targets/help.targ
+test:
 
-all::
-	$(MAKE) ACTION=$@ _action
+install:
+	cp muscle $(BINDIR)
+	
+clean:
+	-\rm -f *.o muscle
 
-clean::
-	$(MAKE) -C lxpack portclean
+portclean: clean
+	-\rm -f $(BINDIR)/muscle
diff --git a/src/muscle/muscle3.8.31/src/README.txt b/src/muscle/muscle3.8.31/README.txt
similarity index 100%
rename from src/muscle/muscle3.8.31/src/README.txt
rename to src/muscle/muscle3.8.31/README.txt
diff --git a/src/muscle/muscle3.8.31/src/aligngivenpath.cpp b/src/muscle/muscle3.8.31/aligngivenpath.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/aligngivenpath.cpp
rename to src/muscle/muscle3.8.31/aligngivenpath.cpp
diff --git a/src/muscle/muscle3.8.31/src/aligngivenpathsw.cpp b/src/muscle/muscle3.8.31/aligngivenpathsw.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/aligngivenpathsw.cpp
rename to src/muscle/muscle3.8.31/aligngivenpathsw.cpp
diff --git a/src/muscle/muscle3.8.31/src/aligntwomsas.cpp b/src/muscle/muscle3.8.31/aligntwomsas.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/aligntwomsas.cpp
rename to src/muscle/muscle3.8.31/aligntwomsas.cpp
diff --git a/src/muscle/muscle3.8.31/src/aligntwoprofs.cpp b/src/muscle/muscle3.8.31/aligntwoprofs.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/aligntwoprofs.cpp
rename to src/muscle/muscle3.8.31/aligntwoprofs.cpp
diff --git a/src/muscle/muscle3.8.31/src/aln.cpp b/src/muscle/muscle3.8.31/aln.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/aln.cpp
rename to src/muscle/muscle3.8.31/aln.cpp
diff --git a/src/muscle/muscle3.8.31/src/alpha.cpp b/src/muscle/muscle3.8.31/alpha.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/alpha.cpp
rename to src/muscle/muscle3.8.31/alpha.cpp
diff --git a/src/muscle/muscle3.8.31/src/alpha.h b/src/muscle/muscle3.8.31/alpha.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/alpha.h
rename to src/muscle/muscle3.8.31/alpha.h
diff --git a/src/muscle/muscle3.8.31/src/anchors.cpp b/src/muscle/muscle3.8.31/anchors.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/anchors.cpp
rename to src/muscle/muscle3.8.31/anchors.cpp
diff --git a/src/muscle/muscle3.8.31/src/bittraceback.cpp b/src/muscle/muscle3.8.31/bittraceback.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/bittraceback.cpp
rename to src/muscle/muscle3.8.31/bittraceback.cpp
diff --git a/src/muscle/muscle3.8.31/src/blosum62.cpp b/src/muscle/muscle3.8.31/blosum62.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/blosum62.cpp
rename to src/muscle/muscle3.8.31/blosum62.cpp
diff --git a/src/muscle/muscle3.8.31/src/blosumla.cpp b/src/muscle/muscle3.8.31/blosumla.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/blosumla.cpp
rename to src/muscle/muscle3.8.31/blosumla.cpp
diff --git a/src/muscle/muscle3.8.31/src/clust.cpp b/src/muscle/muscle3.8.31/clust.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/clust.cpp
rename to src/muscle/muscle3.8.31/clust.cpp
diff --git a/src/muscle/muscle3.8.31/src/clust.h b/src/muscle/muscle3.8.31/clust.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/clust.h
rename to src/muscle/muscle3.8.31/clust.h
diff --git a/src/muscle/muscle3.8.31/src/cluster.cpp b/src/muscle/muscle3.8.31/cluster.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/cluster.cpp
rename to src/muscle/muscle3.8.31/cluster.cpp
diff --git a/src/muscle/muscle3.8.31/src/cluster.h b/src/muscle/muscle3.8.31/cluster.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/cluster.h
rename to src/muscle/muscle3.8.31/cluster.h
diff --git a/src/muscle/muscle3.8.31/src/clustset.h b/src/muscle/muscle3.8.31/clustset.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/clustset.h
rename to src/muscle/muscle3.8.31/clustset.h
diff --git a/src/muscle/muscle3.8.31/src/clustsetdf.h b/src/muscle/muscle3.8.31/clustsetdf.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/clustsetdf.h
rename to src/muscle/muscle3.8.31/clustsetdf.h
diff --git a/src/muscle/muscle3.8.31/src/clustsetmsa.h b/src/muscle/muscle3.8.31/clustsetmsa.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/clustsetmsa.h
rename to src/muscle/muscle3.8.31/clustsetmsa.h
diff --git a/src/muscle/muscle3.8.31/src/clwwt.cpp b/src/muscle/muscle3.8.31/clwwt.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/clwwt.cpp
rename to src/muscle/muscle3.8.31/clwwt.cpp
diff --git a/src/muscle/muscle3.8.31/src/color.cpp b/src/muscle/muscle3.8.31/color.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/color.cpp
rename to src/muscle/muscle3.8.31/color.cpp
diff --git a/src/muscle/muscle3.8.31/src/cons.cpp b/src/muscle/muscle3.8.31/cons.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/cons.cpp
rename to src/muscle/muscle3.8.31/cons.cpp
diff --git a/src/muscle/muscle3.8.31/src/diaglist.cpp b/src/muscle/muscle3.8.31/diaglist.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/diaglist.cpp
rename to src/muscle/muscle3.8.31/diaglist.cpp
diff --git a/src/muscle/muscle3.8.31/src/diaglist.h b/src/muscle/muscle3.8.31/diaglist.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/diaglist.h
rename to src/muscle/muscle3.8.31/diaglist.h
diff --git a/src/muscle/muscle3.8.31/src/diffobjscore.cpp b/src/muscle/muscle3.8.31/diffobjscore.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/diffobjscore.cpp
rename to src/muscle/muscle3.8.31/diffobjscore.cpp
diff --git a/src/muscle/muscle3.8.31/src/diffpaths.cpp b/src/muscle/muscle3.8.31/diffpaths.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/diffpaths.cpp
rename to src/muscle/muscle3.8.31/diffpaths.cpp
diff --git a/src/muscle/muscle3.8.31/src/difftrees.cpp b/src/muscle/muscle3.8.31/difftrees.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/difftrees.cpp
rename to src/muscle/muscle3.8.31/difftrees.cpp
diff --git a/src/muscle/muscle3.8.31/src/difftreese.cpp b/src/muscle/muscle3.8.31/difftreese.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/difftreese.cpp
rename to src/muscle/muscle3.8.31/difftreese.cpp
diff --git a/src/muscle/muscle3.8.31/src/distcalc.cpp b/src/muscle/muscle3.8.31/distcalc.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/distcalc.cpp
rename to src/muscle/muscle3.8.31/distcalc.cpp
diff --git a/src/muscle/muscle3.8.31/src/distcalc.h b/src/muscle/muscle3.8.31/distcalc.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/distcalc.h
rename to src/muscle/muscle3.8.31/distcalc.h
diff --git a/src/muscle/muscle3.8.31/src/distfunc.cpp b/src/muscle/muscle3.8.31/distfunc.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/distfunc.cpp
rename to src/muscle/muscle3.8.31/distfunc.cpp
diff --git a/src/muscle/muscle3.8.31/src/distfunc.h b/src/muscle/muscle3.8.31/distfunc.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/distfunc.h
rename to src/muscle/muscle3.8.31/distfunc.h
diff --git a/src/muscle/muscle3.8.31/src/distpwkimura.cpp b/src/muscle/muscle3.8.31/distpwkimura.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/distpwkimura.cpp
rename to src/muscle/muscle3.8.31/distpwkimura.cpp
diff --git a/src/muscle/muscle3.8.31/src/domuscle.cpp b/src/muscle/muscle3.8.31/domuscle.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/domuscle.cpp
rename to src/muscle/muscle3.8.31/domuscle.cpp
diff --git a/src/muscle/muscle3.8.31/src/dosp.cpp b/src/muscle/muscle3.8.31/dosp.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/dosp.cpp
rename to src/muscle/muscle3.8.31/dosp.cpp
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diff --git a/src/muscle/muscle3.8.31/src/nwdasmall.cpp b/src/muscle/muscle3.8.31/nwdasmall.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/nwdasmall.cpp
rename to src/muscle/muscle3.8.31/nwdasmall.cpp
diff --git a/src/muscle/muscle3.8.31/src/nwrec.cpp b/src/muscle/muscle3.8.31/nwrec.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/nwrec.cpp
rename to src/muscle/muscle3.8.31/nwrec.cpp
diff --git a/src/muscle/muscle3.8.31/src/nwsmall.cpp b/src/muscle/muscle3.8.31/nwsmall.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/nwsmall.cpp
rename to src/muscle/muscle3.8.31/nwsmall.cpp
diff --git a/src/muscle/muscle3.8.31/src/objscore.cpp b/src/muscle/muscle3.8.31/objscore.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/objscore.cpp
rename to src/muscle/muscle3.8.31/objscore.cpp
diff --git a/src/muscle/muscle3.8.31/src/objscore.h b/src/muscle/muscle3.8.31/objscore.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/objscore.h
rename to src/muscle/muscle3.8.31/objscore.h
diff --git a/src/muscle/muscle3.8.31/src/objscore2.cpp b/src/muscle/muscle3.8.31/objscore2.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/objscore2.cpp
rename to src/muscle/muscle3.8.31/objscore2.cpp
diff --git a/src/muscle/muscle3.8.31/src/objscoreda.cpp b/src/muscle/muscle3.8.31/objscoreda.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/objscoreda.cpp
rename to src/muscle/muscle3.8.31/objscoreda.cpp
diff --git a/src/muscle/muscle3.8.31/src/onexception.cpp b/src/muscle/muscle3.8.31/onexception.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/onexception.cpp
rename to src/muscle/muscle3.8.31/onexception.cpp
diff --git a/src/muscle/muscle3.8.31/src/options.cpp b/src/muscle/muscle3.8.31/options.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/options.cpp
rename to src/muscle/muscle3.8.31/options.cpp
diff --git a/src/muscle/muscle3.8.31/src/outweights.cpp b/src/muscle/muscle3.8.31/outweights.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/outweights.cpp
rename to src/muscle/muscle3.8.31/outweights.cpp
diff --git a/src/muscle/muscle3.8.31/src/pam200mafft.cpp b/src/muscle/muscle3.8.31/pam200mafft.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/pam200mafft.cpp
rename to src/muscle/muscle3.8.31/pam200mafft.cpp
diff --git a/src/muscle/muscle3.8.31/src/params.cpp b/src/muscle/muscle3.8.31/params.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/params.cpp
rename to src/muscle/muscle3.8.31/params.cpp
diff --git a/src/muscle/muscle3.8.31/src/params.h b/src/muscle/muscle3.8.31/params.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/params.h
rename to src/muscle/muscle3.8.31/params.h
diff --git a/src/muscle/muscle3.8.31/src/phy.cpp b/src/muscle/muscle3.8.31/phy.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/phy.cpp
rename to src/muscle/muscle3.8.31/phy.cpp
diff --git a/src/muscle/muscle3.8.31/src/phy2.cpp b/src/muscle/muscle3.8.31/phy2.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/phy2.cpp
rename to src/muscle/muscle3.8.31/phy2.cpp
diff --git a/src/muscle/muscle3.8.31/src/phy3.cpp b/src/muscle/muscle3.8.31/phy3.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/phy3.cpp
rename to src/muscle/muscle3.8.31/phy3.cpp
diff --git a/src/muscle/muscle3.8.31/src/phy4.cpp b/src/muscle/muscle3.8.31/phy4.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/phy4.cpp
rename to src/muscle/muscle3.8.31/phy4.cpp
diff --git a/src/muscle/muscle3.8.31/src/phyfromclust.cpp b/src/muscle/muscle3.8.31/phyfromclust.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/phyfromclust.cpp
rename to src/muscle/muscle3.8.31/phyfromclust.cpp
diff --git a/src/muscle/muscle3.8.31/src/phyfromfile.cpp b/src/muscle/muscle3.8.31/phyfromfile.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/phyfromfile.cpp
rename to src/muscle/muscle3.8.31/phyfromfile.cpp
diff --git a/src/muscle/muscle3.8.31/src/physeq.cpp b/src/muscle/muscle3.8.31/physeq.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/physeq.cpp
rename to src/muscle/muscle3.8.31/physeq.cpp
diff --git a/src/muscle/muscle3.8.31/src/phytofile.cpp b/src/muscle/muscle3.8.31/phytofile.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/phytofile.cpp
rename to src/muscle/muscle3.8.31/phytofile.cpp
diff --git a/src/muscle/muscle3.8.31/src/posgap.cpp b/src/muscle/muscle3.8.31/posgap.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/posgap.cpp
rename to src/muscle/muscle3.8.31/posgap.cpp
diff --git a/src/muscle/muscle3.8.31/src/ppscore.cpp b/src/muscle/muscle3.8.31/ppscore.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/ppscore.cpp
rename to src/muscle/muscle3.8.31/ppscore.cpp
diff --git a/src/muscle/muscle3.8.31/src/profdb.cpp b/src/muscle/muscle3.8.31/profdb.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/profdb.cpp
rename to src/muscle/muscle3.8.31/profdb.cpp
diff --git a/src/muscle/muscle3.8.31/src/profile.cpp b/src/muscle/muscle3.8.31/profile.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/profile.cpp
rename to src/muscle/muscle3.8.31/profile.cpp
diff --git a/src/muscle/muscle3.8.31/src/profile.h b/src/muscle/muscle3.8.31/profile.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/profile.h
rename to src/muscle/muscle3.8.31/profile.h
diff --git a/src/muscle/muscle3.8.31/src/profilefrommsa.cpp b/src/muscle/muscle3.8.31/profilefrommsa.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/profilefrommsa.cpp
rename to src/muscle/muscle3.8.31/profilefrommsa.cpp
diff --git a/src/muscle/muscle3.8.31/src/progalign.cpp b/src/muscle/muscle3.8.31/progalign.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/progalign.cpp
rename to src/muscle/muscle3.8.31/progalign.cpp
diff --git a/src/muscle/muscle3.8.31/src/progress.cpp b/src/muscle/muscle3.8.31/progress.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/progress.cpp
rename to src/muscle/muscle3.8.31/progress.cpp
diff --git a/src/muscle/muscle3.8.31/src/progressivealign.cpp b/src/muscle/muscle3.8.31/progressivealign.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/progressivealign.cpp
rename to src/muscle/muscle3.8.31/progressivealign.cpp
diff --git a/src/muscle/muscle3.8.31/src/pwpath.cpp b/src/muscle/muscle3.8.31/pwpath.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/pwpath.cpp
rename to src/muscle/muscle3.8.31/pwpath.cpp
diff --git a/src/muscle/muscle3.8.31/src/pwpath.h b/src/muscle/muscle3.8.31/pwpath.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/pwpath.h
rename to src/muscle/muscle3.8.31/pwpath.h
diff --git a/src/muscle/muscle3.8.31/src/readmx.cpp b/src/muscle/muscle3.8.31/readmx.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/readmx.cpp
rename to src/muscle/muscle3.8.31/readmx.cpp
diff --git a/src/muscle/muscle3.8.31/src/realigndiffs.cpp b/src/muscle/muscle3.8.31/realigndiffs.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/realigndiffs.cpp
rename to src/muscle/muscle3.8.31/realigndiffs.cpp
diff --git a/src/muscle/muscle3.8.31/src/realigndiffse.cpp b/src/muscle/muscle3.8.31/realigndiffse.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/realigndiffse.cpp
rename to src/muscle/muscle3.8.31/realigndiffse.cpp
diff --git a/src/muscle/muscle3.8.31/src/redblack.cpp b/src/muscle/muscle3.8.31/redblack.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/redblack.cpp
rename to src/muscle/muscle3.8.31/redblack.cpp
diff --git a/src/muscle/muscle3.8.31/src/refine.cpp b/src/muscle/muscle3.8.31/refine.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/refine.cpp
rename to src/muscle/muscle3.8.31/refine.cpp
diff --git a/src/muscle/muscle3.8.31/src/refinehoriz.cpp b/src/muscle/muscle3.8.31/refinehoriz.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/refinehoriz.cpp
rename to src/muscle/muscle3.8.31/refinehoriz.cpp
diff --git a/src/muscle/muscle3.8.31/src/refinesubfams.cpp b/src/muscle/muscle3.8.31/refinesubfams.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/refinesubfams.cpp
rename to src/muscle/muscle3.8.31/refinesubfams.cpp
diff --git a/src/muscle/muscle3.8.31/src/refinetree.cpp b/src/muscle/muscle3.8.31/refinetree.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/refinetree.cpp
rename to src/muscle/muscle3.8.31/refinetree.cpp
diff --git a/src/muscle/muscle3.8.31/src/refinetreee.cpp b/src/muscle/muscle3.8.31/refinetreee.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/refinetreee.cpp
rename to src/muscle/muscle3.8.31/refinetreee.cpp
diff --git a/src/muscle/muscle3.8.31/src/refinevert.cpp b/src/muscle/muscle3.8.31/refinevert.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/refinevert.cpp
rename to src/muscle/muscle3.8.31/refinevert.cpp
diff --git a/src/muscle/muscle3.8.31/src/refinew.cpp b/src/muscle/muscle3.8.31/refinew.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/refinew.cpp
rename to src/muscle/muscle3.8.31/refinew.cpp
diff --git a/src/muscle/muscle3.8.31/src/releases.txt b/src/muscle/muscle3.8.31/releases.txt
similarity index 100%
rename from src/muscle/muscle3.8.31/src/releases.txt
rename to src/muscle/muscle3.8.31/releases.txt
diff --git a/src/muscle/muscle3.8.31/src/savebest.cpp b/src/muscle/muscle3.8.31/savebest.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/savebest.cpp
rename to src/muscle/muscle3.8.31/savebest.cpp
diff --git a/src/muscle/muscle3.8.31/src/scoredist.cpp b/src/muscle/muscle3.8.31/scoredist.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/scoredist.cpp
rename to src/muscle/muscle3.8.31/scoredist.cpp
diff --git a/src/muscle/muscle3.8.31/src/scoregaps.cpp b/src/muscle/muscle3.8.31/scoregaps.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/scoregaps.cpp
rename to src/muscle/muscle3.8.31/scoregaps.cpp
diff --git a/src/muscle/muscle3.8.31/src/scorehistory.cpp b/src/muscle/muscle3.8.31/scorehistory.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/scorehistory.cpp
rename to src/muscle/muscle3.8.31/scorehistory.cpp
diff --git a/src/muscle/muscle3.8.31/src/scorehistory.h b/src/muscle/muscle3.8.31/scorehistory.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/scorehistory.h
rename to src/muscle/muscle3.8.31/scorehistory.h
diff --git a/src/muscle/muscle3.8.31/src/scoremx.cpp b/src/muscle/muscle3.8.31/scoremx.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/scoremx.cpp
rename to src/muscle/muscle3.8.31/scoremx.cpp
diff --git a/src/muscle/muscle3.8.31/src/scorepp.cpp b/src/muscle/muscle3.8.31/scorepp.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/scorepp.cpp
rename to src/muscle/muscle3.8.31/scorepp.cpp
diff --git a/src/muscle/muscle3.8.31/src/seq.cpp b/src/muscle/muscle3.8.31/seq.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/seq.cpp
rename to src/muscle/muscle3.8.31/seq.cpp
diff --git a/src/muscle/muscle3.8.31/src/seq.h b/src/muscle/muscle3.8.31/seq.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/seq.h
rename to src/muscle/muscle3.8.31/seq.h
diff --git a/src/muscle/muscle3.8.31/src/seqvect.cpp b/src/muscle/muscle3.8.31/seqvect.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/seqvect.cpp
rename to src/muscle/muscle3.8.31/seqvect.cpp
diff --git a/src/muscle/muscle3.8.31/src/seqvect.h b/src/muscle/muscle3.8.31/seqvect.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/seqvect.h
rename to src/muscle/muscle3.8.31/seqvect.h
diff --git a/src/muscle/muscle3.8.31/src/setblosumweights.cpp b/src/muscle/muscle3.8.31/setblosumweights.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/setblosumweights.cpp
rename to src/muscle/muscle3.8.31/setblosumweights.cpp
diff --git a/src/muscle/muscle3.8.31/src/setgscweights.cpp b/src/muscle/muscle3.8.31/setgscweights.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/setgscweights.cpp
rename to src/muscle/muscle3.8.31/setgscweights.cpp
diff --git a/src/muscle/muscle3.8.31/src/setnewhandler.cpp b/src/muscle/muscle3.8.31/setnewhandler.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/setnewhandler.cpp
rename to src/muscle/muscle3.8.31/setnewhandler.cpp
diff --git a/src/muscle/muscle3.8.31/src/spfast.cpp b/src/muscle/muscle3.8.31/spfast.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/spfast.cpp
rename to src/muscle/muscle3.8.31/spfast.cpp
diff --git a/src/muscle/muscle3.8.31/src/sptest.cpp b/src/muscle/muscle3.8.31/sptest.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/sptest.cpp
rename to src/muscle/muscle3.8.31/sptest.cpp
diff --git a/src/muscle/muscle3.8.31/src/Makefile b/src/muscle/muscle3.8.31/src/Makefile
deleted file mode 100644
index 9631dab..0000000
--- a/src/muscle/muscle3.8.31/src/Makefile
+++ /dev/null
@@ -1,11 +0,0 @@
-include ../../../../config/auto.conf
-
-all: muscle install 
-
-muscle:
-	chmod +x ./mk
-	(export CXX=$(CXX) && ./mk)
-
-install:
-	cp muscle $(BINDIR)
-	
diff --git a/src/muscle/muscle3.8.31/src/stabilize.cpp b/src/muscle/muscle3.8.31/stabilize.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/stabilize.cpp
rename to src/muscle/muscle3.8.31/stabilize.cpp
diff --git a/src/muscle/muscle3.8.31/src/subfam.cpp b/src/muscle/muscle3.8.31/subfam.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/subfam.cpp
rename to src/muscle/muscle3.8.31/subfam.cpp
diff --git a/src/muscle/muscle3.8.31/src/subfams.cpp b/src/muscle/muscle3.8.31/subfams.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/subfams.cpp
rename to src/muscle/muscle3.8.31/subfams.cpp
diff --git a/src/muscle/muscle3.8.31/src/svnmods.h b/src/muscle/muscle3.8.31/svnmods.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/svnmods.h
rename to src/muscle/muscle3.8.31/svnmods.h
diff --git a/src/muscle/muscle3.8.31/src/svnversion.h b/src/muscle/muscle3.8.31/svnversion.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/svnversion.h
rename to src/muscle/muscle3.8.31/svnversion.h
diff --git a/src/muscle/muscle3.8.31/src/sw.cpp b/src/muscle/muscle3.8.31/sw.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/sw.cpp
rename to src/muscle/muscle3.8.31/sw.cpp
diff --git a/src/muscle/muscle3.8.31/src/termgaps.cpp b/src/muscle/muscle3.8.31/termgaps.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/termgaps.cpp
rename to src/muscle/muscle3.8.31/termgaps.cpp
diff --git a/src/muscle/muscle3.8.31/src/textfile.cpp b/src/muscle/muscle3.8.31/textfile.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/textfile.cpp
rename to src/muscle/muscle3.8.31/textfile.cpp
diff --git a/src/muscle/muscle3.8.31/src/textfile.h b/src/muscle/muscle3.8.31/textfile.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/textfile.h
rename to src/muscle/muscle3.8.31/textfile.h
diff --git a/src/muscle/muscle3.8.31/src/threewaywt.cpp b/src/muscle/muscle3.8.31/threewaywt.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/threewaywt.cpp
rename to src/muscle/muscle3.8.31/threewaywt.cpp
diff --git a/src/muscle/muscle3.8.31/src/timing.h b/src/muscle/muscle3.8.31/timing.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/timing.h
rename to src/muscle/muscle3.8.31/timing.h
diff --git a/src/muscle/muscle3.8.31/src/tomhydro.cpp b/src/muscle/muscle3.8.31/tomhydro.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/tomhydro.cpp
rename to src/muscle/muscle3.8.31/tomhydro.cpp
diff --git a/src/muscle/muscle3.8.31/src/traceback.cpp b/src/muscle/muscle3.8.31/traceback.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/traceback.cpp
rename to src/muscle/muscle3.8.31/traceback.cpp
diff --git a/src/muscle/muscle3.8.31/src/tracebackopt.cpp b/src/muscle/muscle3.8.31/tracebackopt.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/tracebackopt.cpp
rename to src/muscle/muscle3.8.31/tracebackopt.cpp
diff --git a/src/muscle/muscle3.8.31/src/tracebacksw.cpp b/src/muscle/muscle3.8.31/tracebacksw.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/tracebacksw.cpp
rename to src/muscle/muscle3.8.31/tracebacksw.cpp
diff --git a/src/muscle/muscle3.8.31/src/tree.h b/src/muscle/muscle3.8.31/tree.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/tree.h
rename to src/muscle/muscle3.8.31/tree.h
diff --git a/src/muscle/muscle3.8.31/src/treefrommsa.cpp b/src/muscle/muscle3.8.31/treefrommsa.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/treefrommsa.cpp
rename to src/muscle/muscle3.8.31/treefrommsa.cpp
diff --git a/src/muscle/muscle3.8.31/src/types.h b/src/muscle/muscle3.8.31/types.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/types.h
rename to src/muscle/muscle3.8.31/types.h
diff --git a/src/muscle/muscle3.8.31/src/typetostr.cpp b/src/muscle/muscle3.8.31/typetostr.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/typetostr.cpp
rename to src/muscle/muscle3.8.31/typetostr.cpp
diff --git a/src/muscle/muscle3.8.31/src/unixio.h b/src/muscle/muscle3.8.31/unixio.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/unixio.h
rename to src/muscle/muscle3.8.31/unixio.h
diff --git a/src/muscle/muscle3.8.31/src/upgma2.cpp b/src/muscle/muscle3.8.31/upgma2.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/upgma2.cpp
rename to src/muscle/muscle3.8.31/upgma2.cpp
diff --git a/src/muscle/muscle3.8.31/src/usage.cpp b/src/muscle/muscle3.8.31/usage.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/usage.cpp
rename to src/muscle/muscle3.8.31/usage.cpp
diff --git a/src/muscle/muscle3.8.31/src/validateids.cpp b/src/muscle/muscle3.8.31/validateids.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/validateids.cpp
rename to src/muscle/muscle3.8.31/validateids.cpp
diff --git a/src/muscle/muscle3.8.31/src/version.txt b/src/muscle/muscle3.8.31/version.txt
similarity index 100%
rename from src/muscle/muscle3.8.31/src/version.txt
rename to src/muscle/muscle3.8.31/version.txt
diff --git a/src/muscle/muscle3.8.31/src/vtml2.cpp b/src/muscle/muscle3.8.31/vtml2.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/vtml2.cpp
rename to src/muscle/muscle3.8.31/vtml2.cpp
diff --git a/src/muscle/muscle3.8.31/src/writescorefile.cpp b/src/muscle/muscle3.8.31/writescorefile.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/writescorefile.cpp
rename to src/muscle/muscle3.8.31/writescorefile.cpp
diff --git a/src/prokov/Makefile b/src/prokov/Makefile
index 2669b78..eedfcf0 100755
--- a/src/prokov/Makefile
+++ b/src/prokov/Makefile
@@ -25,6 +25,3 @@ include ../../config/targets/help.targ
 
 all::
 	$(MAKE) ACTION=$@ _action
-
-clean::
-	$(MAKE) -C lxpack portclean