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package Bio::MUST::Apps::TwoScalp; |
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# ABSTRACT: Main class for two-scalp tool |
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$Bio::MUST::Apps::TwoScalp::VERSION = '0.201810'; |
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use strict; |
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use warnings; |
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use Bio::MUST::Apps::SlaveAligner::Local; |
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use Bio::MUST::Apps::TwoScalp::Seq2Seq; |
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use Bio::MUST::Apps::TwoScalp::Profile2Profile; |
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use Bio::MUST::Apps::TwoScalp::Seqs2Profile; |
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use Bio::MUST::Apps::TwoScalp::AlignAll; |
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1; |
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__END__ |
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=pod |
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=head1 NAME |
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Bio::MUST::Apps::TwoScalp - Main class for two-scalp tool |
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=head1 VERSION |
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version 0.201810 |
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=head1 SYNOPSIS |
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# get documentation |
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$ two-scalp.pl --man |
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# align unaligned sequences within provided example ALI file |
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$ two-scalp.pl test/PTHR22663.ali --out=-ts |
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=head1 DESCRIPTION |
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C<two-scapl.pl> is an application to align or re-align sequences in existing |
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multiple sequences alignments (FASTA or ALI file formats). Its main engine is |
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BLAST L<https://blast.ncbi.nlm.nih.gov/>. |
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Note that only alignable regions of the sequences are added to the alignment, |
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which may lead to discarding low-conserved regions. Moreover, some sequences |
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can generate multiple aligned fragments (BLAST HSPs). If you do not like this |
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behavior, C<two-scalp.pl> is not for you! |
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=head1 AUTHOR |
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Denis BAURAIN <denis.baurain@uliege.be> |
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=head1 COPYRIGHT AND LICENSE |
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This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN. |
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This is free software; you can redistribute it and/or modify it under |
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the same terms as the Perl 5 programming language system itself. |
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=cut |