glmark2 is a benchmark for OpenGL (ES) 2.0. It uses only the subset of the
OpenGL 2.0 API that is compatible with OpenGL ES 2.0.
SysBench is a modular, cross-platform and multi-threaded benchmark tool
for evaluating OS parameters that are important for a system running a
database under intensive load.
The idea of this benchmark suite is to quickly get an impression about
system performance without setting up complex database benchmarks or
even without installing a database at all.
Current features allow to test the following system parameters:
* file I/O performance
* scheduler performance
* memory allocation and transfer speed
* POSIX threads implementation performance
* database server performance (OLTP benchmark)
Primarily written for MySQL server benchmarking, SysBench will be
further extended to support multiple database backends, distributed
benchmarks and third-party plug-in modules.
BLAT is a bioinformatics software tool which performs rapid mRNA/DNA and
cross-species protein alignments. BLAT is more accurate and 500 times
faster than popular existing tools for mRNA/DNA alignments and 50 times
faster for protein alignments at sensitivity settings typically used
when comparing vertebrate sequences. (Source: Kent, W.J. 2002. BLAT --
The BLAST-Like Alignment Tool. Genome Research 4: 656-664.
http://dx.doi.org/10.1101/gr.229202)
BLAT is not BLAST. DNA BLAT works by keeping an index of the entire
genome (but not the genome itself) in memory. Since the index takes up a
bit less than a gigabyte of RAM, BLAT can deliver high performance on a
reasonably priced Linux box.
Consed is a tool for viewing and editing sequence assemblies made by phrap,
and includes Autofinish which will automatically choose finishing reads.
A standalone program for mapping and aligning cDNA sequences to a
genome. The program maps and aligns a single sequence with minimal
startup time and memory requirements, and provides fast batch
processing of large sequence sets. The program generates accurate
gene structures, even in the presence of substantial polymorphisms
and sequence errors, without using probabilistic splice site models.
Methodology underlying the program includes a minimal sampling
strategy for genomic mapping, oligomer chaining for approximate
alignment, sandwich DP for splice site detection, and microexon
identification with statistical significance testing.
p5-Bio-Das-Lite is an implementation of a client for the DAS protocol (XML
over HTTP primarily for biological-data).
Bioperl-run contain modules that provides a PERL interface to various
bioinformatics applications. This allows various applications to be used
with common Bioperl objects.
Samtools implements various utilities for post-processing alignments in the
SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
with bcftools), and a simple alignment viewer.
A set of tools written in Perl and C++ for working with VCF files, such as
those generated by the 1000 Genomes Project.
atlc is a program designed for finding the properties (characteristic
impedance, inductance per meter, capacitance per meter, velocity
factor, electric field distribution) of any transmission line with
2 or 3 conductors (i.e. a normal line or coupler). It uses the
finite difference method to determine these properties, and can
handle any cross section.
The program atlc needs to know shape of the transmission line's
cross section. This cross section is stored in a data file, which
happens to be a Windows bitmap file. The bitmap file is read by
atlc, following which the program performs the analysis. Look in
/usr/local/share/examples/atlc for some examples.