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/**********************************************************************
* File: dist2tree.h
* Author: Kevin Howe
* Copyright (C) Genome Research Limited, 2002-
*-------------------------------------------------------------------
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*-------------------------------------------------------------------
* NOTES:
* This program can be used to generate neighbour-joining
* trees given a distance matrix file.
* The matrix file should be in phylip format; the application was
* originally coded to compare the efficiency of the writer's
* implementation of neighbourjoining with that of phylip's
* 'neighbor' program. The tree is writtento stdout in New Hants
* format.
**********************************************************************/
#ifndef _DIST2TREE
#define _DIST2TREE
#include "align.h"
#include "options.h"
#include "util.h"
#include "cluster.h"
#include "buildtree.h"
/********************** function prototypes ***************************/
/*********************************************************************
FUNCTION: maketree_neighbourjoin
DESCRIPTION:
Given a file handle to a distance matrix, creates and prints a neighbour
joining phlogenetic tree for the sequences in the alignment
RETURNS: void
ARGS:
A file handle to a distance matrix (in 'phylip' format)
NOTES:
*********************************************************************/
void maketree_neighbourjoin( FILE * );
#endif
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