Quick start

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Here are some quick entry points to help orient you towards common tasks:

Find documentation about all the methods available to a particular object

You should see the Deobfuscator to find out this info. Unfortunately, some modules are better documented than others - we are trying to work on this.

Process a sequence file to get the sequence or to find the exon locations

See Bio::SeqIO and the SeqIO HOWTO and the Feature-Annotation HOWTO.

Count the number of hits for each query from a BLAST report

See Bio::SearchIO and the SearchIO HOWTO. Bio::SearchIO lists all the file formats that BioPerl can parse.

Process a Clustalw formatted alignment

Use Bio::AlignIO to parse multiple sequence alignments. If one wanted to convert the alignment into a NEXUS multiple alignment format for running with PAUP and MrBayes, use Bio::AlignIO::nexus. If one wanted to run a PHYLIP program use the Bio::AlignIO::phylip module to convert the alignment into PHYLIP multiple alignment format.

Read a phylogenetic tree file

See Bio::TreeIO and the Trees HOWTO for reading and writing tree objects. One can interrogate trees as well and there are several supported tree functions in Bio::Tree::TreeFunctionsI.

Parse MEME output and manipulate motif information

See Bio::Matrix::PSM and Bio::AlignIO::meme.

Check to see if a certain script has already been written

Go to the Bioperl scripts page.

Parse the output from Gene prediction programs

There are parsers for Genscan, MZEF, Sim4, Exonerate, Genewise, Genomewise. Tools like SNAP, Twinscan, Genezilla produce GFF output which can be processed with Bio::Tools::GFF.

Run population genetics tests

The PopGen HOWTO provides an introduction to the PopGen modules. Statistics are calculated with Bio::PopGen::Statistics while the Bio::PopGen::Utilities provides functions for converting alignments to Bio::PopGen::Populations.

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