1Bio::Tools::Run::PiseApUpsleircaCtoinotnr:i:bpuatme(d3B)Pieor:l:TDoooclusm:e:nRtuant:i:oPniseApplication::pam(3)
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NAME

6       Bio::Tools::Run::PiseApplication::pam
7

SYNOPSIS

9         #
10

DESCRIPTION

12       Bio::Tools::Run::PiseApplication::pam
13
14             Bioperl class for:
15
16               PAM     Generate a PAM matrix
17
18             Parameters:
19
20               (see also:
21                 http://bioweb.pasteur.fr/seqanal/interfaces/pam.html
22                for available values):
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24                       pam (String)
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26                       scale (Float)
27                               Scale 0. < scale <= 1000 (-s)
28
29                       x (Integer)
30                               Substitution value for X with any other letter (-x)
31
32                       distance (Integer)
33                               PAM distance (from 2 to 511)
34

FEEDBACK

36       Mailing Lists
37
38       User feedback is an integral part of the evolution of this and other
39       Bioperl modules. Send your comments and suggestions preferably to the
40       Bioperl mailing list.  Your participation is much appreciated.
41
42         bioperl-l@bioperl.org                  - General discussion
43         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
44
45       Reporting Bugs
46
47       Report bugs to the Bioperl bug tracking system to help us keep track of
48       the bugs and their resolution. Bug reports can be submitted via the
49       web:
50
51         http://bugzilla.open-bio.org/
52

AUTHOR

54       Catherine Letondal (letondal@pasteur.fr)
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57       Copyright (C) 2003 Institut Pasteur & Catherine Letondal.  All Rights
58       Reserved.
59
60       This module is free software; you can redistribute it and/or modify it
61       under the same terms as Perl itself.
62

DISCLAIMER

64       This software is provided "as is" without warranty of any kind.
65

SEE ALSO

67       ·   http://bioweb.pasteur.fr/seqanal/interfaces/pam.html
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69       ·   Bio::Tools::Run::PiseApplication
70
71       ·   Bio::Tools::Run::AnalysisFactory::Pise
72
73       ·   Bio::Tools::Run::PiseJob
74
75       new
76
77        Title   : new()
78        Usage   : my $pam = Bio::Tools::Run::PiseApplication::pam->new($location, $email, @params);
79        Function: Creates a Bio::Tools::Run::PiseApplication::pam object.
80                  This method should not be used directly, but rather by
81                  a Bio::Tools::Run::AnalysisFactory::Pise instance.
82                  my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
83                  my $pam = $factory->program('pam');
84        Example : -
85        Returns : An instance of Bio::Tools::Run::PiseApplication::pam.
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89perl v5.8.8                       2007-B0i4o-:1:9Tools::Run::PiseApplication::pam(3)
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