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Fig. 1 | BMC Bioinformatics

Fig. 1

From: BpWrapper: BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines

Fig. 1

Four command-line utilities in BpWrapper. a bioseq reads sequences (in FASTA format as the default) as inputs, renders them into Bio::Seq objects in BioPerl (blue), and generates sequence statistics (green) or a modified FASTA file (purple). b bioaln reads a sequence alignment (in CLUSTALW format as the default) as input, renders them into a Bio::SimpleAlign object in BioPerl, and generates alignment statistics or a modified alignment. c biopop reads allelic sequences (in FASTA format as the default) as inputs, renders them into Bio::PopGen objects, and generates SNP (single-nucleotide polymorphism) statistics. d biotree reads a phylogenetic tree (in NEWICK format as the default) as inputs, renders it into a Bio::Tree::Tree object, and generates tree statistics or a modified tree. Note that since the Bio::PopGen class in BioPerl inherits the Bio::SimpleAlign class, which in turn inherits the Bio::Seq class, options in bioseq are applicable to alignments as well as to allelic sequences and options in bioaln are applicable to allelic sequence alignments. Documentation of these utilities are self-contained through the Perl POD mechanism and viewable on the command line through the “perldoc” command or the “--help”, “-h”, or “--man” options. A reference card of all options and their usage is provided in the Additional file 1

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