bp_blast2tree(1p) [debian man page]

BP_BLAST2TREE(1p)					User Contributed Perl Documentation					 BP_BLAST2TREE(1p)

NAME

       tree_from_seqsearch - builds a phylogenetic tree based on a sequence search (FastA,BLAST,HMMER)

DESCRIPTION

       This script requires that the bioperl-run pkg be also installed.

perl v5.14.2							    2012-03-02							 BP_BLAST2TREE(1p)

Bio::Tools::HMMER::Set(3pm)				User Contributed Perl Documentation			       Bio::Tools::HMMER::Set(3pm)

NAME

       Bio::Tools::HMMER::Set - Set of identical domains from HMMER matches

SYNOPSIS

	   # get a Set object probably from the results object
	   print "Bits score over set ",$set->bits," evalue ",$set->evalue,"
";

	   foreach $domain ( $set->each_Domain ) {
	       print "Domain start ",$domain->start," end ",$domain->end,"
";
	   }

DESCRIPTION

       Represents a set of HMMER domains hitting one sequence. HMMER reports two different scores, a per sequence total score (and evalue) and a
       per domain score and evalue. This object represents a collection of the same domain with the sequence bits score and evalue. (these
       attributes are also on the per domain scores, which you can get there).

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
       of the Bioperl mailing lists.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       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.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution.Bug reports can be submitted via the
       web:

	https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Ewan Birney
       Email birney-at-ebi.ac.uk

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   add_Domain
	Title	: add_Domain
	Usage	: $set->add_Domain($domain)
	Function: adds the domain to the list
	Returns : nothing
	Args	: A Bio::Tools::HMMER::Domain object

   each_Domain
	Title	: each_Domain
	Usage	: foreach $domain ( $set->each_Domain() )
	Function: returns an array of domain objects in this set
	Returns : array
	Args	: none

   name
	Title	: name
	Usage	: $obj->name($newval)
	Function:
	Example :
	Returns : value of name
	Args	: newvalue (optional)

   desc
	Title	: desc
	Usage	: $obj->desc($newval)
	Function:
	Example :
	Returns : value of desc
	Args	: newvalue (optional)

   accession
	Title	: accession
	Usage	: $obj->accession($newval)
	Function:
	Example :
	Returns : value of accession
	Args	: newvalue (optional)

   bits
	Title	: bits
	Usage	: $obj->bits($newval)
	Function:
	Example :
	Returns : value of bits
	Args	: newvalue (optional)

   evalue
	Title	: evalue
	Usage	: $obj->evalue($newval)
	Function:
	Example :
	Returns : value of evalue
	Args	: newvalue (optional)

perl v5.14.2							    2012-03-02					       Bio::Tools::HMMER::Set(3pm)