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Viewing changes to src/clustal/muscle_upgma.h

Committer: Package Import Robot
Author(s): Olivier Sallou
Date: 2011-12-14 11:21:56 UTC
Revision ID: package-import@ubuntu.com-20111214112156-y3chwm0t4yn2nevm

Tags: upstream-1.0.3

Import upstream version 1.0.3

files added:

AUTHORS

COPYING

ChangeLog

Doxyfile

Doxyfile.in

INSTALL

Makefile.am

Makefile.in

NEWS

README

TODO

aclocal.m4

clustalo.pc.in

config.guess

config.sub

configure

configure.ac

depcomp

install-sh

ltmain.sh

m4/ax_openmp.m4

m4/ax_prefix_config_h.m4

m4/libtool.m4

m4/ltoptions.m4

m4/ltsugar.m4

m4/ltversion.m4

m4/lt~obsolete.m4

missing

src/Makefile.am

src/Makefile.in

src/clustal

src/clustal-omega-config.h

src/clustal-omega.c

src/clustal-omega.h

src/clustal/Makefile.am

src/clustal/Makefile.in

src/clustal/hhalign_wrapper.c

src/clustal/hhalign_wrapper.h

src/clustal/ktuple_pair.c

src/clustal/ktuple_pair.h

src/clustal/list.c

src/clustal/list.h

src/clustal/log.c

src/clustal/log.h

src/clustal/mbed.c

src/clustal/mbed.h

src/clustal/muscle_tree.c

src/clustal/muscle_tree.h

src/clustal/muscle_upgma.c

src/clustal/muscle_upgma.h

src/clustal/pair_dist.c

src/clustal/pair_dist.h

src/clustal/progress.c

src/clustal/progress.h

src/clustal/queue.h

src/clustal/seq.c

src/clustal/seq.h

src/clustal/symmatrix.c

src/clustal/symmatrix.h

src/clustal/tree.c

src/clustal/tree.h

src/clustal/util.c

src/clustal/util.h

src/clustal/weights.c

src/clustal/weights.h

src/clustalo-api-test.c

src/config.h.in

src/hhalign

src/hhalign/Makefile.am

src/hhalign/Makefile.in

src/hhalign/general.h

src/hhalign/hash-C.h

src/hhalign/hash.h

src/hhalign/hhalign.cpp

src/hhalign/hhalign.h

src/hhalign/hhalignment-C.h

src/hhalign/hhalignment.h

src/hhalign/hhdecl-C.h

src/hhalign/hhfullalignment-C.h

src/hhalign/hhfullalignment.h

src/hhalign/hhfunc-C.h

src/hhalign/hhfunc.h

src/hhalign/hhhalfalignment-C.h

src/hhalign/hhhalfalignment.h

src/hhalign/hhhit-C.h

src/hhalign/hhhit.h

src/hhalign/hhhitlist-C.h

src/hhalign/hhhitlist.h

src/hhalign/hhhmm-C.h

src/hhalign/hhhmm.h

src/hhalign/hhmatrices-C.h

src/hhalign/hhutil-C.h

src/hhalign/list-C.h

src/hhalign/list.h

src/hhalign/util-C.h

src/kmpp

src/kmpp/KMeans.cpp

src/kmpp/KMeans.h

src/kmpp/KmTree.cpp

src/kmpp/KmTree.h

src/kmpp/KmUtils.cpp

src/kmpp/KmUtils.h

src/kmpp/Makefile.am

src/kmpp/Makefile.in

src/main.cpp

src/mymain.c

src/mymain.h

src/squid

src/squid/00README

src/squid/COPYRIGHT

src/squid/LICENSE

src/squid/Makefile.am

src/squid/Makefile.in

src/squid/a2m.c

src/squid/aligneval.c

src/squid/alignio.c

src/squid/clustal.c

src/squid/clustalo.README

src/squid/cluster.c

src/squid/dayhoff.c

src/squid/eps.c

src/squid/file.c

src/squid/getopt.c

src/squid/gki.c

src/squid/gki.h

src/squid/gsi.c

src/squid/gsi.h

src/squid/gsi64.c

src/squid/gsi64.h

src/squid/hsregex.c

src/squid/iupac.c

src/squid/msa.c

src/squid/msa.h

src/squid/msf.c

src/squid/phylip.c

src/squid/revcomp.c

src/squid/rk.c

src/squid/rk.h

src/squid/selex.c

src/squid/seqencode.c

src/squid/shuffle.c

src/squid/sqerror.c

src/squid/sqfuncs.h

src/squid/sqio.c

src/squid/squid-1.9g.tar.gz

src/squid/squid.h

src/squid/squidcore.c

src/squid/sre_ctype.c

src/squid/sre_math.c

src/squid/sre_random.c

src/squid/sre_random.h

src/squid/sre_string.c

src/squid/ssi.c

src/squid/ssi.h

src/squid/stack.c

src/squid/stockholm.c

src/squid/stockholm.h

src/squid/stopwatch.c

src/squid/stopwatch.h

src/squid/translate.c

src/squid/types.c

src/squid/vectorops.c

src/squid/vectorops.h

src/squid/version.h

src/squid/weight.c

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src/clustal/muscle_upgma.h

/* This the fast UPGMA algorithm (O(N^2)) as implemented in Bob Edgar's

* Muscle (UPGMA2.cpp; version 3.7) ported to pure C.

* Muscle's code is public domain and so is this code here.

* From http://www.drive5.com/muscle/license.htm:

* """

* MUSCLE is public domain software

* The MUSCLE software, including object and source code and

* documentation, is hereby donated to the public domain.

* Disclaimer of warranty

* THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND,

* EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION IMPLIED

* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE

* """

* RCS $Id: muscle_upgma.h 193 2011-02-07 15:45:21Z andreas $

#ifndef CLUSTALO_UPGMA_H

#define CLUSTALO_UPGMA_H

#include "symmatrix.h"

#include "muscle_tree.h"

enum linkage_e {

LINKAGE_MIN,

LINKAGE_AVG,

LINKAGE_MAX,

LINKAGE_NEIGHBORJOINING,

LINKAGE_BIASED

};

typedef enum linkage_e linkage_t;

void MuscleUpgma2(tree_t *tree, symmatrix_t *distmat,

linkage_t linkage, char **names);

#endif

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