Blast Similarity Matrix

Algorithm::NeedlemanWunsch is a sequence alignment with configurable scoring. SYNOPSIS use Algorithm::NeedlemanWunsch; sub score_sub { if (!@_) { return -2; # gap penalty } return ($_[0] eq $_[1]) ? 1 : -1; } my $matcher = Algorithm::NeedlemanWunsch->new(&score_sub); my $score =...

A MATLAB spectral clustering package to handle large data sets (200,000 RCV1 data) on a 4GB memory general machine. We implement various ways of approximating the dense similarity matrix, including nearest neighbors and the Nystrom method.

MayaChemTools is a collection of command line Perl scripts to work with SD files, CSV/TSV text files, Sequence/Alignments files, PDB files, and databases: - splitting, joining, merging, and sorting SD and text files; merging text files into SD files; splitting SD files into MDL MOL files; -...


Platforms: Windows, Mac, *nix, Perl, BSD Solaris

The Matrix Reloaded screensaver is a freeware openGL matrix screen saver that truly captivates the spirit of The Matrix movie, Matrix Reloaded and Matrix Revolutions sequels. Featuring photos of heroes & foes (Neo, Morpheus, Trinity, Agent Smith, etc presented in a cool slideshow), matrix code...

Morello Matrix Calculator is a simple, low cost utility for manipulating matrices of real numbers. It is as easy to use as a pocket calculator, but can perform most standard matrix operations for matrices up to 20 elements square. It also supports cut and paste operations allowing matrix data to...


Platforms: Windows

Solve a matrix or system of linear equations using the Gauss method.


Platforms: Windows

The Matrix guitars screensaver, The classic green matrix screen, but this time done with guitars. No spyware, no adware, just the text www.guitar-academy.com, small in the corner of the screen. This screen saver is completely free. No cons . . . .


Platforms: Windows

Similarity is a useful program that helps you to find and remove similar, duplicate musical files (MP3, WMA, OGG, ASF, WAV, FLAC, APE, WV) with the same or similar sound content, music tags (ID3,WMF,Vorbis). This is the best program where similarity of a sound part is checked, not just music tags...


Platforms: Windows

Domino Blast project is a physics-based driving/demolition game with a childrens toys theme. Domino Blast is a hybrid driving and destruction game with a childrens toys theme. Its environments consist of buildings constructed from domino tiles and a player-controllable toy car. The objective of...


Platforms: *nix

Bio::Index::Blast is a Perl module with indexes Blast reports and supports retrieval based on query accession(s). SYNOPSIS use strict; use Bio::Index::Blast; my ($indexfile,$file1, $file2); my $index = new Bio::Index::Blast(-filename => $indexfile, -write_flag => 1);...


Platforms: *nix

Meta Matrix Library is a modular designed collection of C libraries. Meta Matrix Library was developed as part of the Free Finite Element Package to provide easy and consistent access to numerical linear algebra software for sparse and dense matrices. The dense matrix and vector operations of...


Platforms: *nix

Math::Zap::Matrix is a Perl module for 3*3 matrix manipulation. Synopsis Example t/matrix.t #_ Matrix _____________________________________________________________ # Test 3*3 matrices # philiprbrenan@yahoo.com, 2004, Perl License...


Platforms: *nix

exmats goal is to provide an easy to use, yet very efficient matrix library. Overloaded operators allow to write algebraic expressions like v=A*u +u in C++, instead of bunch of boring functions. This syntactic sugar comes with runtime cost, one way to eliminate the overhead is to use Expression...


Platforms: *nix

WordNet::Similarity::Visual is a Perl extension for providing visualization tools for WordNet::Similarity. SYNOPSIS Basic Usage Example use WordNet::Similarity::Visual; $gui = WordNet::Similarity::Visual->new; $gui->initialize; This package provides a graphical extension for...


Platforms: *nix

Bio::Matrix::PSM::InstanceSite is a PSM site occurance. SYNOPSIS use Bio::Matrix::PSM::InstanceSite; #You can get an InstanceSite object either from a file: my ($instances,$matrix)=$SomePSMFile->parse_next; #or from memory my %params=(seq=>TATAAT, id=>"TATAbox1",...


Platforms: *nix

WordNet::Similarity::PathFinder is a Perl module to implement path finding methods (by node counting) for WordNet::Similarity measures of semantic relatedness. SYNOPSIS use WordNet::QueryData; my $wn = WordNet::QueryData->new; use WordNet::Similarity::PathFinder; my $obj =...


Platforms: *nix

WordNet::Similarity::vector_pairs is a Perl module for computing semantic relatedness of word senses using second order co-occurrence vectors of glosses of the word senses. SYNOPSIS use WordNet::Similarity::vector_pairs; use WordNet::QueryData; my $wn = WordNet::QueryData->new(); my...


Platforms: *nix

WordNet::Similarity is a collection of Perl modules for computing measures of semantic relatedness. SYNOPSIS Basic Usage Example use WordNet::QueryData; use WordNet::Similarity::path; my $wn = WordNet::QueryData->new; my $measure = WordNet::Similarity::path->new ($wn); my $value =...


Platforms: *nix

Math::Matrix can multiply and invert Matrices. The following methods are available: new Constructor arguments are a list of references to arrays of the same length. The arrays are copied. The method returns undef in case of error. $a = new Math::Matrix ([rand,rand,rand],...


Platforms: *nix

Cylindrical BLAST Viewer is a small, easy to use application specially designed to offer users a 3D viewer that arranges BLAST hits and other bioinformatics-related alignments in a rotating, cylindrical display. Basically this tool arranges the alignments in a cylinder, which spins past the eye...


Platforms: Windows