File Coverage

blib/lib/Bio/MUST/Apps/TwoScalp.pm
Criterion Covered Total %
statement 21 21 100.0
branch n/a
condition n/a
subroutine 7 7 100.0
pod n/a
total 28 28 100.0


line stmt bran cond sub pod time code
1             package Bio::MUST::Apps::TwoScalp;
2             # ABSTRACT: Main class for two-scalp tool
3             $Bio::MUST::Apps::TwoScalp::VERSION = '0.231010';
4 1     1   263349 use strict;
  1         7  
  1         28  
5 1     1   6 use warnings;
  1         12  
  1         32  
6              
7 1     1   577 use Bio::MUST::Apps::SlaveAligner::Local;
  1         4767058  
  1         38  
8 1     1   724 use Bio::MUST::Apps::TwoScalp::Seq2Seq;
  1         8  
  1         44  
9 1     1   691 use Bio::MUST::Apps::TwoScalp::Profile2Profile;
  1         5  
  1         47  
10 1     1   686 use Bio::MUST::Apps::TwoScalp::Seqs2Profile;
  1         4  
  1         43  
11 1     1   571 use Bio::MUST::Apps::TwoScalp::AlignAll;
  1         4  
  1         53  
12              
13             1;
14              
15             __END__
16              
17             =pod
18              
19             =head1 NAME
20              
21             Bio::MUST::Apps::TwoScalp - Main class for two-scalp tool
22              
23             =head1 VERSION
24              
25             version 0.231010
26              
27             =head1 SYNOPSIS
28              
29             # get documentation
30             $ two-scalp.pl --man
31              
32             # align unaligned sequences within provided example ALI file
33             $ two-scalp.pl test/PTHR22663.ali --out=-ts
34              
35             =head1 DESCRIPTION
36              
37             C<two-scapl.pl> is an application to align or re-align sequences in existing
38             multiple sequences alignments (FASTA or ALI file formats). Its main engine is
39             BLAST L<https://blast.ncbi.nlm.nih.gov/>.
40              
41             Note that only alignable regions of the sequences are added to the alignment,
42             which may lead to discarding low-conserved regions. Moreover, some sequences
43             can generate multiple aligned fragments (BLAST HSPs). If you do not like this
44             behavior, C<two-scalp.pl> is not for you!
45              
46             =head1 AUTHOR
47              
48             Denis BAURAIN <denis.baurain@uliege.be>
49              
50             =head1 COPYRIGHT AND LICENSE
51              
52             This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN.
53              
54             This is free software; you can redistribute it and/or modify it under
55             the same terms as the Perl 5 programming language system itself.
56              
57             =cut