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muscle_upgma.h
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/* This the fast UPGMA algorithm (O(N^2)) as implemented in Bob Edgar's
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* Muscle (UPGMA2.cpp; version 3.7) ported to pure C.
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*
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* Muscle's code is public domain and so is this code here.
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*
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* From http://www.drive5.com/muscle/license.htm:
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* """
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* MUSCLE is public domain software
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*
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* The MUSCLE software, including object and source code and
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* documentation, is hereby donated to the public domain.
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*
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* Disclaimer of warranty
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* THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND,
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* EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION IMPLIED
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* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* """
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*
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*/
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/*
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* RCS $Id: muscle_upgma.h 193 2011-02-07 15:45:21Z andreas $
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*/
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#ifndef CLUSTALO_UPGMA_H
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#define CLUSTALO_UPGMA_H
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#include "
symmatrix.h
"
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#include "
muscle_tree.h
"
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enum
linkage_e
{
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LINKAGE_MIN
,
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LINKAGE_AVG
,
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LINKAGE_MAX
,
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LINKAGE_NEIGHBORJOINING
,
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LINKAGE_BIASED
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};
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typedef
enum
linkage_e
linkage_t
;
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void
MuscleUpgma2
(
tree_t
*tree,
symmatrix_t
*distmat,
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linkage_t
linkage,
char
**names);
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#endif
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