1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
|
/***********************************************************************
* File: aln2dist.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 produces a distance matrix in phylip format for the
* given alignment file. The optional -k flag is used to determine
* whether Kimura's tranlation is used to hopefully obtain more
* accurate distances. The matrix is written to stdout
***********************************************************************/
#ifndef _ALN2DIST
#define _ALN2DIST
#include "options.h"
#include "util.h"
#include "align.h"
#include "cluster.h"
/********************** function prototypes ***************************/
/*********************************************************************
FUNCTION: generate_matrix_matrixmaker
DESCRIPTION:
Given a fule handle to an alignment, creates and prints a
distance matrix for the sequences in the alignment in phylip format
to stdout
RETURNS: void
ARGS:
An open alignment FILE
NOTES:
*********************************************************************/
void generate_DistanceMatrix_matrixmaker( FILE * );
#endif
|
