Sequences

JFinisher is software for alignment, editing and manipulation of biological sequences. It aims to assist in the finishing of genome assembly. Starting from a reference sequence, the program align contigs using Smith-Waterman local alignment algoritm with auxiliary methods, allowing management of...

JPhylo is a Java based visualization program used to display sequences of phylogenetic trees.

A viewer for image sequences, aimed to be a professional tool for viewing animation frames rendered with 2D and 3D editing software. It is cross-platform, fast, supports many image formats and OpenGL rendering.


Platforms: Windows, Mac, Linux

This script shows a few simple methods implementing multiple hotkey support for emacs-like hotkey sequences.


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

DJV Imaging provides professional movie playback software for film production, VFX, and computer animation. Features Available for Linux, Mac OS, Solaris, and Windows Playback both image sequences and movie files Support for industry standard file formats including Cineon, DPX, OpenEXR,...


Platforms: *nix

Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.


Platforms: Windows, Mac, Linux

Molevolve is a Java library for running a Genetic Algorithm to model the 3-dimensional structures of peptide chains from amino-acid sequences. Client code can specify its own peptide chain model, fitness functions and GA operations. Requires JDK 1.5.


Platforms: Windows, Mac, Linux

OraDoc is an open source Java based tool for creation of Oracle database documentation in HTML format similar to JavaDoc supporting tables (including foreign key relations), views, object types, sequences and packages.


Platforms: Windows, Mac, Linux

ProteinMusic is a Java program converting DNA sequences into music. The original idea for this project came from R. D. King at the University of Wales, Aberystwyth and C. G Angus from the Shamen (King, R.D. & Angus, C.G. (1996)).


Platforms: Windows, Mac, BSD, Linux

Highlight converts sourcecode to HTML, XHTML, RTF, LaTeX, TeX, SVG, BBCode and terminal escape sequences with coloured syntax highlighting. Language definitions and colour themes are customizable. Highlight was designed to offer a flexible but easy to use syntax highlighter for several output...


Platforms: Linux

ReverseComplement is a handy, easy to use, simple application specially designed to help you determine the reverse, complement, and reverse complement of DNA and RNA sequences.


Platforms: Windows

OrientationChecker is a simple, Java based application specially designed to help you check and alter the orientation of 16S rRNA gene sequences.


Platforms: Windows

Allows stdin or files specified on the command line to be printed from aremote terminal using ANSI escape sequences.Inspired by the ansiprt.c component of U Wash's PINE.


Platforms: Windows, Mac, Linux

CRF is a Java implementation of Conditional Random Fields, an algorithm for learning from labeled sequences of examples. It also includes an implementation of Maximum Entropy learning.


Platforms: Windows, Mac, Linux

The fourth MATLAB Programming Contest, MasterminddlT«, ran from September 17-21, 2001.The challenge was to write an algorithm to solve a variation of the classic MasterminddlT« puzzle. Each entry did its best to determine unknown sequences of colored pegs.This submission includes all the...


Platforms: Matlab

NemoDB is the Php class which provide simple, quasi relational database.Features:- tables can store text, images etc.- automatic column value compression and decomp.;- sequences, DBA account, stored procedures;


Platforms: PHP

Accepts a regular expression as an argument and any matches found (stdin) will be highlighted (stdout) using shell color escape sequences. Good for looking through logs/monitoring console output/etc.


Platforms: Windows, Mac, Linux

MOTIFINFO = GIBBSMOTIFSAMPLER(SEQARRAY,MOTIFVECTOR,ALPHABET,OPTIONS) Searches for the motifs in a set of sequences via Gibbs sampling. seqArray is a cell vector of sequence strings. motifVector is a vector of uniformly-spaced motif widths you wish to optimize. The program iterates over these...


Platforms: Matlab

A cross-platform Christmas light show scheduler built on wxWidgets. Plays Vixen and LOR S2 sequences. Compatible with LOR, D-Light, DMX, and Renard controllers.


Platforms: Mac

Use this to encode bit sequences with the duobinary signaling technique or the modified duobinary signaling technique.Duobinary signaling is a three level signaling scheme that uses intersymbol interference in a controlled way instead of trying to eliminate it.


Platforms: Matlab