Clustal Omega  1.1.0
src/clustal/muscle_upgma.h
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00001 /* This the fast UPGMA algorithm (O(N^2)) as implemented in Bob Edgar's
00002  * Muscle (UPGMA2.cpp; version 3.7) ported to pure C.
00003  *
00004  * Muscle's code is public domain and so is this code here.
00005  *
00006  * From http://www.drive5.com/muscle/license.htm:
00007  * """
00008  * MUSCLE is public domain software
00009  *
00010  * The MUSCLE software, including object and source code and
00011  * documentation, is hereby donated to the public domain.
00012  *
00013  * Disclaimer of warranty
00014  * THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND,
00015  * EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION IMPLIED
00016  * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
00017  * """
00018  *
00019  */
00020 
00021 /*
00022  *  RCS $Id: muscle_upgma.h 193 2011-02-07 15:45:21Z andreas $
00023  */
00024 
00025 #ifndef CLUSTALO_UPGMA_H
00026 #define CLUSTALO_UPGMA_H
00027 
00028 #include "symmatrix.h"
00029 #include "muscle_tree.h"
00030 
00031 enum linkage_e {
00032     LINKAGE_MIN,
00033     LINKAGE_AVG,
00034     LINKAGE_MAX,
00035     LINKAGE_NEIGHBORJOINING,
00036     LINKAGE_BIASED
00037 };
00038 typedef enum linkage_e linkage_t;
00039 
00040 void MuscleUpgma2(tree_t *tree, symmatrix_t *distmat,
00041                    linkage_t linkage, char **names);
00042 
00043 #endif