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Versatile omics shotgun and amplicon sequencing read simulator
Grinder is a versatile program to create random shotgun and amplicon sequence libraries based on DNA, RNA or proteic reference sequences provided in a FASTA file. . Grinder can produce genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, metaproteomic shotgun and amplicon datasets from current sequencing technologies such as Sanger, 454, Illumina. These simulated datasets can be used to test the accuracy of bioinformatic tools under specific hypothesis, e.g. with or without sequencing errors, or with low or high community diversity. Grinder may also be used to help decide between alternative sequencing methods for a sequence-based project, e.g. should the library be paired-end or not, how many reads should be sequenced.
complete front-end for MPlayer - icon themes
Qt Mplayer front-end, with basic features like playing videos, DVDs, and VCDs to more advanced features like support for MPlayer filters and more. One of the most interesting features of SMPlayer: it remembers the settings of all files you play. So you start to watch a movie but you have to leave... don't worry, when you open that movie again it will resume at the same point you left it, and with the same settings: audio track, subtitles, volume... . This package contains additional icon themes.
Multitouch X input driver
This X input driver provides gestures support for multitouch touchpads, in particular those with integrated button.
Perl extension for running and parsing NCBI's BLAST 2.x
NHGRI::Blastall will enable usage of BLAST out of a Perl script, if BLAST2 or WU-BLAST are installed locally. Main features are: * run BLAST (also via network, which requires blastcl3) * BLAST single sequences against each other or against a given library * format databases * mask out repetitive DNA * read, parse and filter existing BLAST reports
Database of transitive groups for GAP
GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas. In the example text, gap is used to analyse Rubik's Cube using group theory. A kernel implements a Pascal-like language. . This package contains the database of transitive groups.
module to convert POD to the Markdown file format
Pod::Markdown is a Perl module that parses Plain Old Documentation (POD) and converts it into the Markdown text format. It subclasses Pod::Parser, so it supports all of its commands, too. . Markdown is a markup language to convert structured text into (X)HTML. Its main design goal is to make the input text as readable as possible. For this, the syntax is highly inspired by the format of plain text email. Markdown supports features like headers, *emphasis*, code blocks, blockquotes and links. For maximum flexibility, it also allows embedding HTML tags, both within paragraphs (eg. <span>), and at block level (<div>, <table>).