forked from johannesgerer/jburkardt-f
-
Notifications
You must be signed in to change notification settings - Fork 1
/
read_align.html
141 lines (115 loc) · 3.08 KB
/
read_align.html
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
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
<html>
<head>
<title>
READ_ALIGN - Convert an alignment to PIR format
</title>
</head>
<body bgcolor="#EEEEEE" link="#CC0000" alink="#FF3300" vlink="#000055">
<h1 align = "center">
READ_ALIGN <br> Convert an alignment to PIR format
</h1>
<hr>
<p>
<b>READ_ALIGN</b>
is a FORTRAN90 program which
reads a file
containing information about a multiple sequence alignment, and
writes out the relevant information to another file using
the PIR format, by Des Higgins.
</p>
<p>
The reason for converting to the PIR format is to use
the <a href = "../../f_src/distances/distances.html">DISTANCES</a> program.
</p>
<h3 align = "center">
Languages:
</h3>
<p>
<b>READ_ALIGN</b> is available in
<a href = "../../f77_src/read_align/read_align.html">a FORTRAN77 version</a> and
<a href = "../../f_src/read_align/read_align.html">a FORTRAN90 version</a>.
</p>
<h3 align = "center">
Related Data and Programs:
</h3>
<p>
<a href = "../../f_src/distances/distances.html">
DISTANCES</a>,
a FORTRAN90 program which
can read a file in PIR format and create a distance matrix.
</p>
<p>
<a href = "../../f_src/spacer/spacer.html">
SPACER</a>,
a FORTRAN90 program which
can read a distance matrix and perform a principal component analysis.
</p>
<p>
<a href = "../../f_src/spacer_data_convert/spacer_data_convert.html">
SPACER_DATA_CONVERT</a>,
a FORTRAN90 program which
can read a multiple sequence alignment file and write out the
relevant information into a file in PIR format.
</p>
<h3 align = "center">
Author:
</h3>
<p>
Des Higgins,<br>
EMBL Data Library,<br>
April 1992.
</p>
<h3 align = "center">
Source Code:
</h3>
<p>
<ul>
<li>
<a href = "read_align.f90">read_align.f90</a>, the source code;
</li>
<li>
<a href = "read_align.sh">read_align.sh</a>,
commands to compile and load the source code;
</li>
</ul>
</p>
<h3 align = "center">
Examples and Tests:
</h3>
<p>
<ul>
<li>
<a href = "clustal.dat">clustal.dat</a>, a CLUSTAL alignment file;
</li>
<li>
<a href = "clustal.pir">clustal.pir</a>, the converted alignment file;
</li>
</ul>
</p>
<h3 align = "center">
List of Routines:
</h3>
<p>
<ul>
<li>
<b>READ_ALIGN</b> reads a multiple alignment file and rewrites it in PIR format.
</li>
<li>
<b>BLANK_LINE</b> looks for a "blank" line.
</li>
<li>
<b>TIMESTAMP</b> prints the current YMDHMS date as a time stamp.
</li>
</ul>
</p>
<p>
You can go up one level to <a href = "../f_src.html">
the FORTRAN90 source codes</a>.
</p>
<hr>
<i>
Last revised on 15 December 2007.
</i>
<!-- John Burkardt -->
</body>
</html>