BPPPHYSAMP(1) General Commands Manual BPPPHYSAMP(1)NAME
bppphysamp - Phylogenetic sampling with Bio++
SYNOPSIS
bppphysamp [options]
AVAILABILITY
All UNIX flavors
DESCRIPTION
bppphysamp samples a sequence alignment according to a given phylogenetic tree, in order to control the set of redundancy in the data.
OPTIONS
You should refer to 'info bppsuite' or to the online manual of bppsuite for a complete list of available options.
--noninteractive
generates output for redirection in a file.
param=file
reads a file for loading options
AUTHOR
The Bio++ Development Team.
LOCAL BPPPHYSAMP(1)
Check Out this Related Man Page
Bio::PhyloNetwork::Factory(3pm) User Contributed Perl Documentation Bio::PhyloNetwork::Factory(3pm)NAME
Bio::PhyloNetwork::Factory - Module to sequentially generate Phylogenetic Networks
SYNOPSIS
use strict;
use warnings;
use Bio::PhyloNetwork;
use Bio::PhyloNetwork::Factory;
# Will generate sequentially all the 4059 binary tree-child phylogenetic
# networks with 4 leaves
my $factory=Bio::PhyloNetwork::Factory->new(-numleaves=>4);
my @nets;
while (my $net=$factory->next_network()) {
push @nets,$net;
print "".(scalar @nets).": ".$net->eNewick()."
";
}
DESCRIPTION
Sequentially builds a (binary tree-child) phylogenetic network each time next_network is called.
AUTHOR
Gabriel Cardona, gabriel(dot)cardona(at)uib(dot)es
SEE ALSO
Bio::PhyloNetwork
APPENDIX
The rest of the documentation details each of the object methods.
new
Title : new
Usage : my $factory = new Bio::PhyloNetwork::Factory();
Function: Creates a new Bio::PhyloNetwork::Factory
Returns : Bio::PhyloNetwork::RandomFactory
Args : -numleaves => integer
OR
-leaves => reference to an array (of leaves names)
-numhybrids => integer [default = numleaves -1]
-recurse => boolean [optional]
Returns a Bio::PhyloNetwork::Factory object. Such an object will sequentially create binary tree-child phylogenetic networks each time
next_network is called.
If the parameter -leaves=>@leaves is given, then the set of leaves of these networks will be @leaves. If it is given the parameter
-numleaves=>$numleaves, then the set of leaves will be "l1"..."l$numleaves".
If the parameter -numhybrids=>$numhybrids is given, then the generated networks will have at most $numhybrids hybrid nodes. Note that,
necessarily, $numhybrids < $numleaves.
If the parameter -recurse=>1 is given, then all networks with number of hybrid nodes less or equal to $numhybrids will be given; otherwise
only those with exactly $numhybrids hybrid nodes.
next_network
Title : next_network
Usage : my $net=$factory->next_network()
Function: returns a network
Returns : Bio::PhyloNetwork
Args : none
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