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Christopher Fields
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Bio::Cluster::SequenceFamily - Sequence Family object


  use Bio::Cluster::SequenceFamily;

  use Bio::SeqIO;
  use Bio::Cluster::SequenceFamily;
  use File::Spec;

  my $file =  File::Spec->catfile('t','data','swiss.dat');
  my $seqio= Bio::SeqIO->new(-format => 'swiss',
                            -file => $file);
  my @mem;
  while(my $seq = $seqio->next_seq){
    push @mem, $seq;

  #create the family
  my $family = Bio::Cluster::SequenceFamily->new(
          -description=>"Family Description Here",

  #access the family

  foreach my $mem ($family->get_members){
    print $mem->display_id."\t".$mem->desc."\n";

  #select members if members have a Bio::Species Object

  my @mem = $family->get_members(-binomial=>"Homo sapiens");
  @mem = $family->get_members(-ncbi_taxid => 9606);
  @mem = $family->get_members(-common_name=>"Human");
  @mem = $family->get_members(-species=>"sapiens");
  @mem = $family->get_members(-genus=>"Homo");


This is a simple Family object that may hold any group of object. For more specific families, one should derive from FamilyI.


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AUTHOR - Shawn Hoon

Email shawnh@fugu-sg.org


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


 Title   : new
 Usage   : my $family = Bio::Cluster::SequenceFamily->new(
                             -description=>"Family Description Here",
 Function: Constructor for SequenceFamily object
 Returns : Bio::Cluster::SequenceFamily object

See Bio::Cluster::SequenceFamily.


 Title   : version
 Usage   : $family->version("1.0");
 Function: get/set for version
 Returns : a string version of the family generated. 


 Title   : annotation_score
 Usage   : $family->annotation_score(100);
 Function: get/set for annotation_score which
           represent the confidence in which the 
           consensus description has been assigned
           to the family.
 Returns : Bio::SimpleAlign

See Bio::SimpleAlign


 Title   : alignment
 Usage   : $family->alignment($align);
 Function: get/set for an alignment object representing
           the multiple alignment of the members of the family.
 Returns : Bio::SimpleAlign

See Bio::SimpleAlign


 Title   : tree
 Usage   : $family->tree($tree);
 Function: get/set for an tree object representing
           the phylogenetic tree of the family. 
 Returns : Bio::Tree

See Bio::Tree

Bio::Cluster::FamilyI methods


 Title   : family_score
 Usage   : Bio::Cluster::FamilyI->family_score(95);
 Function: get/set for the score of algorithm used to generate
           the family if present

           This is aliased to cluster_score().

 Returns : the score
 Args    : the score


 Title   : family_id
 Usage   : $family->family_id("Family_1"); 
 Function: get/set for family id 

           This is aliased to display_id().

 Returns : a string specifying identifier of the family 

Bio::ClusterI methods


 Title   : display_id
 Usage   : 
 Function: Get/set the display name or identifier for the cluster
 Returns : a string
 Args    : optional, on set the display ID ( a string)


 Title   : description
 Usage   : $fam->description("POLYUBIQUITIN")
 Function: get/set for the consensus description of the cluster
 Returns : the description string 
 Args    : Optional the description string 


 Title   : get_members
 Usage   : Valid criteria:
           $family->get_members(-common_name =>"human");
           $family->get_members(-species     =>"homo sapiens");
           $family->get_members(-ncbi_taxid  => 9606);
           For now, multiple critieria are ORed.

           Will return all members if no criteria are provided.

 Function: get members using methods from L<Bio::Species>
           the phylogenetic tree of the family.
 Returns : an array of objects that are member of this family. 


 Title   : size
 Usage   : $fam->size();
 Function: get/set for the size of the family, 
           calculated from the number of members
 Returns : the size of the family 
 Args    : 


 Title   : cluster_score
 Usage   : $fam->cluster_score(100);
 Function: get/set for cluster_score which
           represent the score in which the clustering
           algorithm assigns to this cluster.
 Returns : a number

Implementation specific methods

  These are mostly for adding/removing/changing.


 Title   : add_members
 Usage   : $fam->add_member([$seq1,$seq1]);
 Function: add members to a family
 Returns : 
 Args    : the member(s) to add, as an array or arrayref


 Title   : remove_members
 Usage   : $fam->remove_members();
 Function: remove all members from a family 
 Returns : the previous array of members
 Args    : none


 Title   : members
 Usage   : $members = $fam->members([$seq1,$seq1]);
 Function: Deprecated. Use add_members() or get_members() instead