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/***********************************************************************
* File: aln2tree.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 constructs a phylogenetic tree from a given align-
* ment file. The process comprises of two phases:
* 1. Construction of a distance matrix. Here, the optional -k
* is used to determine whether Kimura's tranlation is used to
* hopefully obtain more accurate distance
* 2. The construction of the tree. It is printed in New-Hampshire
* format to standard output
***********************************************************************/
#ifndef _ALN2TREE
#define _ALN2TREE
#include "options.h"
#include "util.h"
#include "align.h"
#include "cluster.h"
#include "buildtree.h"
/********************** function prototypes ***************************/
/*********************************************************************
FUNCTION: maketree_treemaker
DESCRIPTION:
Given a fule handle to an alignment, creates and prints a neighbour
joining phlogenetic tree for the sequences in the alignment
RETURNS: void
ARGS:
A file handle to an alignment (should be in MUL format);
NOTES:
*********************************************************************/
void maketree_treemaker( FILE * );
#endif
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