The FASTX-Toolkit is a collection of command line tools for Short-Reads
FASTA/FASTQ files preprocessing.
MrBayes is a program for the Bayesian estimation of phylogeny.
Bayesian inference of phylogeny is based upon a quantity called the
posterior probability distribution of trees, which is the probability of a
tree conditioned on the observations. The conditioning is accomplished
using Bayes's theorem. The posterior probability distribution of trees is
impossible to calculate analytically; instead, MrBayes uses a simulation
technique called Markov chain Monte Carlo (or MCMC) to approximate the
posterior probabilities of trees.
The Lagan Tookit is a set of alignment programs for comparative
genomics. The three main components are a pairwise aligner (LAGAN), a
multiple aligner (M-LAGAN), and a glocal aligner (Shuffle-LAGAN). All
three are based on the CHAOS local alignment tool and combine speed
(regions up to several megabases can be aligned in minutes) with high
accuracy. The results of the alignment can be visualized using the VISTA
visualization tool.
Trimmomatic performs a variety of useful trimming tasks for illumina
NGS paired-end and single ended data.
Alliance is a complete set of free CAD tools and portable libraries
for VLSI design. It includes a VHDL compiler and simulator, logic
synthesis tools, and automatic place and route tools. A complete set
of portable CMOS libraries is provided. Alliance is the result of a
twelve year effort spent at ASIM department of LIP6 laboratory of
the Pierre et Marie Curie University (Paris VI, France).
BrickUtils is a simple utility for builders that use LEGO Digital Designer
or LDraw-compatible CAD for designing models.
LibreCAD is a 2D CAD drawing application based on the community
edition of QCad (www.qcad.org).
This is GDS2, a module for quickly creating programs to read,
write, and manipulate GDS2 (GDSII) stream files.
fcitx-chewing provides Chewing, an intelligent phonetic input method
engine, as a back-end to the Fcitx IM framework.
aprsd is a server daemon that provides Internet gateway and client access
to amateur radio APRS packet data.