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
1.6.3