Bio::SeqEvolution::EvolutionI - the interface for evolving sequences
# not an instantiable class
This is the interface that all classes that mutate sequence objects in constant fashion must implement. A good example is Bio::SeqEvolution::DNAPoint.
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rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
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Heikki Lehvaslaiho E<lt>heikki at bioperl dot orgE<gt>
Additional contributor's names and emails here
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : annotation Usage : $obj->annotation($newval) Function: Get the annotation collection for this annotatable object. Example : Returns : a Bio::AnnotationCollectionI implementing object, or undef Args : on set, new value (a Bio::AnnotationCollectionI implementing object, optional) (an implementation may not support changing the annotation collection)
See Bio::AnnotationCollectionI
Title : seq Usage : $obj->seq($newval) Function: Set the sequence object for the original sequence Returns : The sequence object Args : newvalue (optional)
Setting this will reset mutation and generated mutation counters.
Title : next_seq Usage : $obj->next_seq Function: Evolve the reference sequence to desired level Returns : A new sequence object mutated from the reference sequence Args : -
Title : mutate Usage : $obj->mutate Function: mutate the sequence at the given location according to the model Returns : true Args : integer, start location of the mutation, required argument
Called from next_seq().
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.