Gap Penalty

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 =...

JAligner is an open source Java implementation of the dynamic programming algorithm Smith-Waterman with Gotoh's improvement for biological local pairwise sequence alignment with the affine gap penalty model.

NeoBio project consists of Bioinformatics algorithms in Java. What algorithms? The current version consists mainly of (pairwise) sequence alignment algorithms such as the classical dynamic programming methods of Needleman & Wunsch (global alignment) and Smith & Waterman (local alignment)....


Platforms: *nix

Statistics::Gap Perl module is an adaptation of the Gap Statistic. SYNOPSIS use Statistics::Gap; $predictedk = &gap("prefix", "vec", INPUTMATRIX, "rbr", "h2", 30, 10, rep, 90, 4); OR use Statistics::Gap; $predictedk = &gap("prefix", "vec", INPUTMATRIX, "rbr", "h2", 30, 10, rep, 90, 4,...


Platforms: *nix

AcQuest Programming Solutions is pleased to publish AcQuest Tax Penalty & Interest Evaluator. Designed to run on Windows XP, Vista, & Windows 7 systems, the program will calculate and verify federal tax penalties and interest for individuals, corporations, and employers. Calculates interest and...


Platforms: Windows, Other

In this game, you need to play penalty shootout with the computer. First, choose your team and the computer's team, then the shootout begin. Use the mouse to point to the position you want to shoot to, when you shoot, there may be some deviations so don't go too far. When the computer shoots, you...


Platforms: Windows

A native Macintosh OS X front-end/environment for the GAP computer algebra system. 'Xgap without X11.'


Platforms: Mac

GAP is a Generic Jakarta ANT Project file for the complete building of a Java Application from your source to executable jar by simply modifying a simple properties file with details on your project. No knowlege of ANT is required. Great way for the novic


Platforms: Windows, Mac, Linux

Magmentis is proud to introduce: Fill the Gap Lite, the new free version of this popular software already used by several hundred thousands of children in schools all over the world (and by more than the 30% of primary schools just in the UK) to improve pupils' literacy and spelling skills....


Platforms: Mac

Bio::Tools::Run::PiseApplication::fasta is a Bioperl class for sequence database search. Parameters: fasta (Excl) Fasta program query (Sequence) Query sequence File pipe: seqfile seqtype (Excl) Is it a DNA or protein sequence (-n) protein_db (Excl) Protein Database nucleotid_db...


Platforms: *nix

AVL Array is an STL-like container for C++ that fills the gap between vector (or deque) and list, providing both fast random access and fast insertion/removal, all O(log n). This is not a map; in an avl_array, the "keys" always range from 0 to size-1, and they automatically change on insertion...


Platforms: *nix

THREDDS (short from Thematic Realtime Environmental Distributed Data Services) project is developing middleware to bridge the gap between data providers and data users. The goal is to simplify the discovery and use of scientific data and to allow scientific publications and educational materials...


Platforms: *nix

This is a small utility that cleans up the registry in those cases where huge gaps of whitespace is displayed in the add/remove programs control panel applet. The gap is caused by a badly formatted "DisplayedIcon" entry in the uninstall area of the registry or a bad icon file. We read about the...


Platforms: Windows

The Hot Potatoes suite includes six applications, enabling you to create interactive multiple-choice, short-answer, jumbled-sentence, crossword, matching/ordering and gap-fill exercises for the World Wide Web. Hot Potatoes is not freeware, but it is free of charge for non-profit educational users...


Platforms: Windows

EC Software Help Suite complements the help functions of Borland Delphi and fills the gap between our flagship product Help & Manual and your application. 4 powerful components manage context sensitive help (similar to the help functions of MS Word), the instant implementation of HTML HELP and...


Platforms: Windows

All users who often convert VHS and Beta to digital have to do so with milimetric precision and spend hours in the process. Then there are always small, but irritating, gaps between sound and image so they don+t correspond 100%.To fix this annoying gap is Mi BAO TV 1.9.1 which is a simple and...


Platforms: Windows

JGAP (pronounced "jay-gap") is a genetic algorithms component written in the form of a Java package. JGAP project provides basic genetic mechanisms that can be easily used to apply evolutionary principles to problem solutions. The ground is laid for introducing Genetic Programming to JGAP in the...


Platforms: *nix

iTunes-LAME Encoder bridges the gap between iTunes and the LAME command line encoder. It joins the simple interface of iTunes with the higher quality of the LAME encoder.


Platforms: Mac

Cast Away fills a gap left in iTunes' implementation of Podcasts. Podcast Removal Features: - Separate podcast removal settings per podcast subscription - Separate settings for iTunes and iPod for each podcast - Separate settings for long and short episodes - Separate over-rides, such as keep...


Platforms: Mac

afari Developer was designed to fill the gap between Safari's Web Inspector and the needs of today's web developers. While Web Inspector offers a great variety of tools it lacks support for daily tasks of modern web development. This useful extension provides users with functions such as...


Platforms: Windows