Sequences

OligoLocator is a simple, Java based application designed to identify the position of oligonucleotides within nucleic acid sequences with varying degrees of mismatch between the two. Platforms: Windows

Create matching sequences of birds of the same color and discover the Golden Bird artifact. Explore 3 unique gameplay modes, with various bonuses and surprises. Funny sparrows will try to distract you, by resorting to various tricks, making laugh, gladden, surprise and delight! The game is full... Platforms: Windows

Toolkit to examine the topology of a phylogenetic tree, place amino acid substitutions on specific branches, polarize them and compare amino acid sequences of homologous proteins to answer a wide range of questions about protein evolution. Platforms: Windows, Mac, Linux

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

The Blast2SNP is able to pick out synonymous, non-synonymous mutations and indels from draft assembly sequences by performing BLAST search against the reference ORF sequences. Platforms: Windows, Mac, Linux

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

Cell Motility Analysis Package analyzes timelapse sequences of moving cells. Various quantitites characterizing motility are calculated, including normal velocity of the membrane, cell contact area, and spatio-temporal auto-correlation functions. Platforms: Windows, Mac, BSD, Linux

CisPlusFinder predicts cis-regulatory modules based on perfect local ungapped sequences using comparative sequence data from multiple organisms. An overview of the CisPlusFinder can be found in the flowchart.tif file and is described in the following publication: Pierstorff, N., C.M. Bergman &... Platforms: Mac, BSD

Cleaver is a program for comparing restriction endonuclease digests of orthologous DNA sequences from different taxa. It performs virtual restriction digests and searches for endonucleases that cleave DNA fragments from given taxa but not others. 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

Software to cluster protein sequences into functionally similar groups. Journal reference: http://bioinformatics.oxfordjournals.org/cgi/content/short/24/16/1765 Platforms: Mac, Linux

EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries and provides several layers of annotation based on Entrez Gene to allow the user to highlight useful genes and manage cDNA library projects. Platforms: Windows, Mac, Linux

FSA is a probabilistic multiple sequence alignment algorithm which uses a 'distance-based' approach to aligning homologous protein, RNA or DNA sequences. Platforms: Mac, BSD, Linux

GraphicalOSfp is a python application which aims to collect random data issued by remote systems in IP and TCP sequences. These data are then displayed in a 3D referencial to highlight an attractor of the random engine of the remote machine. Platforms: Mac, Linux

ICRPfinder finds or generates DNA patterns which can include restriction enzyme recognition sites in coding sequences without changing the translated protein sequence. Platforms: Windows, Mac, Linux

Java agent which recognizes 'flows' as unique sequences of instrumented method calls. Runtime statistics are collected for the dynamically detected flows during snapshot interval. The instrumented methods may be set either manually via UI or automatically in drill down mode. The automatic drill... Platforms: Windows, Mac, Linux

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... Platforms: Mac

JPhylo is a Java based visualization program used to display sequences of phylogenetic trees. Platforms: Windows, Mac, Linux

C++ classes for the generation of low-discrepancy sequences used in numerical calculations (Halton, Sobol, Faure and Niederreiter (t,s) sequences, as well as n alpha sequences and pseudo-random number generators). Also classes for some other distributions 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