Alignments

alignlib is a C++ library for computing and manipulating sequence alignments of protein sequences. Most of the functions and classes are exported to python thus permitting easy scripting of complex tasks. Platforms: Mac

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that: * Is flexible enough to store all the alignment information generated by various alignment programs; * Is simple enough to be easily generated by alignment... Platforms: Mac

Welcome to the SRMA home page. SRMA is a short read micro re-aligner for next-generation high throughput sequencing data. Sequence alignment algorithms examine each read independently. When indels occur towards the ends of reads, the alignment can lead to false SNPs as well as improperly placed... Platforms: Mac

CMView is an intervative contact map visualization and analysis tool. The current version is 0.9.6 Please send feedback to stehr ?*A*t molgen.mpg.de Main features: * Combined contact map and 3D structure view (using PyMol) * Various im- and export options: PDB files, Online PDB, Image... Platforms: Mac

jMOTU is a software package for clustering barcode DNA sequence data into molecular operational taxonomic units (MOTU). If you are not sure what a MOTU is, please see the DNA Barcoding pages on our website. jMOTU does the following: *reads input sequences in FASTA or NEXUS format *calculates... Platforms: Mac

Recco analyzes alignments of sequences that evolved subject to recombination and mutation. The analysis provides evidence as to whether a dataset contains recombination, which sequence is a recombinant and where the recombination breakpoints are. The analysis is based on explaining one sequence... Platforms: Mac

Laj is a tool for viewing and manipulating the output from pairwise alignment programs such as blastz. It can display interactive dotplot, pip, and text representations of the alignments, a diagram showing the locations of exons and repeats, and annotation links to other web sites containing... Platforms: Mac

bedtools: a flexible suite of utilities for comparing genomic features. The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.... Platforms: Mac

Taxtastic is software written in python used to build and maintain reference packages-- i.e. collections of reference trees, reference alignments, profiles, and associated taxonomic information. . quickstart . full documentation Platforms: *nix

emageX is an ActiveX based Internet imaging tool incorporating a variety of practical imaging features for convenient online image browsing experience. emageX features the proprietary"single click"innoslide technology using which all the images on a web page are extracted and displayed as an...

RichView is a suite of native Delphi/C++Builder components for displaying, editing and printing hypertext documents. Components support various character attributes (fonts, subscripts/superscripts, colored text background, custom drawn). Documents can contain tables, pictures, images from... Platforms: Windows

RichView is a suite of native Delphi/C++Builder components for displaying, editing and printing hypertext documents. Components support various character attributes (fonts, subscripts/superscripts, colored text background, custom drawn). Documents can contain tables, pictures, images from... Platforms: Windows

Office Diary 2006 is a software application that provides you with the ability of adding, editing and managing your diary,document, publish writings, pictures, and features all under the tree structure. Getting Start Run OfficeDiary.exe Features 1.Clean and intuitive user-friendly interface just... Platforms: Windows

PopupNotify is an ActiveX control provides MSN style popup alerts. Popup alerts fade in and slide up above the taskbar and disappear after a few seconds. Supports transparency, balloon tips, pictures, gradients, sounds, multiple alignments, and more! PopupNotify is fully Unicode capable.... Platforms: Windows

Batch It Ultra is our flagship Batch Image Processor. Now available in Native 32 and 64 Bit. It is a tool which helps you batch resize, change format, rename, add up to 3 text captions, add up to 3 watermarks, apply special effects and adjust photo settings. It also has support printing and... Platforms: Windows, Windows 8, Windows 7, Windows Server

Vendetta Online is a MMORPG (massively multiplayer online role-playing game) from Guild Software Inc. In this game, thousands of people can play together, at the same time, in a single, persistent universe. Players take the form of spaceship pilots within this universe, flying to and fro between... Platforms: *nix

libgtkhtml is a GNOME library for gtkhtml2 module. Installation: The simplest way to compile this package is: 1. `cd to the directory containing the packages source code and type `./configure to configure the package for your system. If youre using `csh on an old version of System V, you... Platforms: *nix

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 =... Platforms: *nix

Gene Inspector is a unique combination of a versatile electronic laboratory research notebook and a comprehensive sequence analysis product. Using GI, the user has the ability to define an entire 'suite of analyses' that can be performed each time they (or anyone in the lab) has a new sequence,... Platforms: Mac

The goal of BioX is to bring easy-to-use sequence analysis to Mac-using biologists. It features graphical editors for sequences and multiple alignments, and supports opening and saving of many different sequence file formats. Analysis functions currently include searching for primers, restriction... Platforms: Mac