Download Shareware and Freeware Software for Windows, Linux, Macintosh, PDA

line Home  |  About Us  |  Link To Us  |  FAQ  |  Contact

Serving Software Downloads in 976 Categories, Downloaded 32.291.837 Times

Bio::Tree::DistanceFactory 1.5.2_102

  Date Added: November 22, 2010  |  Visits: 642

Bio::Tree::DistanceFactory

Report Broken Link
Printer Friendly Version


Product Homepage
Download (72 downloads)

Bio::Tree::DistanceFactory is a Perl module to construct a tree using distance based methods. SYNOPSIS use Bio::Tree::DistanceFactory; use Bio::AlignIO; use Bio::Align::DNAStatistics; my $tfactory = Bio::Tree::DistanceFactory->new(-method => "NJ"); my $stats = Bio::Align::DNAStatistics->new(); my $alnin = Bio::AlignIO->new(-format => clustalw, -file => file.aln); my $aln = $alnin->next_aln; # Of course matrix can come from a different place # like PHYLIP if you prefer, Bio::Matrix::IO should be able # to parse many things my $jcmatrix = $stats->distance(-align => $aln, -method => Jukes-Cantor); my $tree = $tfactory->make_tree($jcmatrix); This is a factory which will construct a phylogenetic tree based on the pairwise sequence distances for a set of sequences. Currently UPGMA (Sokal and Michener 1958) and NJ (Saitou and Nei 1987) tree construction methods are implemented..

Requirements: No special requirements
Platforms: Linux
Keyword: Based Biotreedistancefactory Construct Distance Distancefactory Libraries Perl Module Programming Tree Using
Users rating: 0/10

License: Freeware Size: 5.6 MB
BIO::TREE::DISTANCEFACTORY RELATED
Libraries  -  Cache::Memcached::Tie 0.03
Cache::Memcached::Tie is a Perl module created for using Cache::Memcached as hash. SYNOPSIS #!/usr/bin/perl -w use strict; use Cache::Memcached::Tie; my %hash; my $memd=tie %hash,Cache::Memcached::Tie, {servers=>[192.168.0.77:11211]};...
15.36 KB  
Libraries  -  Alien Perl module 0.91
Alien Perl module package contains external libraries wrapped up for your viewing pleasure! SYNOPSIS perldoc Alien; Alien is a package that exists just to hold together an idea, the idea of Alien:: packages, so there is no code here, just...
10.24 KB  
Libraries  -  OpenGeoDB Perl module 0.4
OpenGeDB Perl module is a module to access the OpenGeoDB database and calculate all ZIP codes in a certain radius..
3.07 KB  
Libraries  -  Tk::PerlInheritanceTree 0.02
Tk::PerlInheritanceTree is a Perl module that displays a graphical representation of the inheritance tree for a given class-name. SYNOPSIS require Tk::PerlInheritanceTree; ... my $inheritance_tree = $main_window->PerlInheritanceTree()->pack;...
4.1 KB  
Libraries  -  AI::DecisionTree 0.08
AI::DecisionTree is Perl module for automatically Learns Decision Trees. SYNOPSIS use AI::DecisionTree; my $dtree = new AI::DecisionTree; # A set of training data for deciding whether to play tennis $dtree->add_instance (attributes =>...
25.6 KB  
Network & Internet  -  MyCMS perl module 1.0
MyCMS perl module provides the MN::CMS Perl module used by the MyCMS. MyCMS perl module contains Perl object classes to manage the data of MyCMS (such as articles, links, and images). MN::CMS is a perl module that allows you to manage an...
16.38 KB  
Libraries  -  ClearCase::SyncTree 0.39
ClearCase::SyncTree is a Perl module that can synchronize a tree of files with a tree of elements. SYNOPSIS # Create a synctree object. my $sync = ClearCase::SyncTree->new; # Tell it where the files are coming from ......
32.77 KB  
Libraries  -  File::RdistByRsync 0.3
File::RdistByRsync is a Perl module that can read rdist distfiles, emulate using rsync. SYNOPSIS use File::RdistByRsync @dist_blocks = parse_rdist($distfile, %options) ($args, $extras, @dist_blocks) = rdist(@ARGV); rsync(@ARGV) perl...
10.24 KB  
Libraries  -  dtRdr::GUI::Wx::SearchTree 0.0.11
dtRdr::GUI::Wx::SearchTree is a Perl module that can display search results as a tree. SYNOPSIS Methods book_root Create a root for the book. $tree->book_root($book); When were displaying multiple books, this will not be the root of...
2.8 MB  
Libraries  -  Pod::HTML_Elements 0.05
Pod::HTML_Elements is a Perl module to convert POD to tree of LWPs HTML::Element and hence HTML or PostScript. SYNOPSIS use Pod::HTML_Elements; my $parser = new Pod::HTML_Elements; $parser->parse_from_file($pod,foo.html); my $parser = new...
9.22 KB  
NEW DOWNLOADS IN PROGRAMMING, LIBRARIES
Programming  -  Cedalion for Linux 0.2.6
Cedalion is a programming language that allows its users to add new abstractions and define (and use) internal DSLs. Its innovation is in the fact that it uses projectional editing to allow the new abstractions to have no syntactic limitations.
471.04 KB  
Programming  -  Math::GMPf 0.29
Math::GMPf - perl interface to the GMP library's floating point (mpf) functions.
30.72 KB  
Programming  -  Net::Wire10 1.08
Net::Wire10 is a Pure Perl connector that talks to Sphinx, MySQL and Drizzle servers. Net::Wire10 implements the low-level network protocol, alias the MySQL wire protocol version 10, necessary for talking to one of the aforementioned...
30.72 KB  
Programming  -  logilab-common 0.56.2
a bunch of modules providing low level functionnalities shared among some python projects devel Please note that some of the modules have some extra dependencies. For instance, logilab.common.db will require a db-api 2.0 compliant...
174.08 KB  
Programming  -  OpenSSL for linux 1.0.0a
The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolkit implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a...
3.83 MB  
Libraries  -  wolfSSL 3.15.3
The wolfSSL embedded SSL/TLS library is a lightweight SSL library written in ANSI standard C and targeted for embedded and RTOS environments - primarily because of its small size, speed, and feature set. It is commonly used in standard operating...
3.88 MB  
Libraries  -  EuGTK 4.8.9
Makes it easy to develop good- looking, fast, cross-platform programs that run on Linux, OS X, and Windows. Euphoria is a very fast interpreted/compiled language with straight-forward syntax. EuGTK allows programming in a clean, object-oriented...
10.68 MB  
Libraries  -  Linux User Group Library Manager 1.0
The LUG Library Manager is a project to help Linux User Groups start their own library. A LUG library is helpful to the community at large because it increases access to information, and gives everyone the opportunity to become more knowledgeable.
5.35 KB  
Libraries  -  Module::MakefilePL::Parse 0.12
Module::MakefilePL::Parse is a Perl module to parse required modules from Makefile.PL. SYNOPSIS use Module::MakefilePL::Parse; open $fh, Makefile.PL; $parser = Module::MakefilePL::Parse->new( join("", ) ); $info = $parser->required;...
8.19 KB  
Libraries  -  sqlpp 0.06
sqlpp Perl package is a SQL preprocessor. sqlpp is a conventional cpp-alike preprocessor taught to understand SQL ( PgSQL, in particular) syntax specificities. In addition to the standard #define/#ifdef/#else/#endif cohort, provides also...
10.24 KB