Migrate estimates effective population sizes and past migration rates between
two or "n" populations assuming a migration matrix model with asymmetric
migration rates and different subpopulation sizes. The n-population migrate
can use sequence data, microsatellite data or electrophoretic data.
PSI/88 Version 1.0 by W. L. Jorgensen & D. L. Severance
To plot wavefunctions in three dimensions from
semi-empirical and most popular ab initio basis sets.
Valence semi-empirical, STO-3G, 3-21++G(*) and
6-31++G(d,p) basis sets are implemented for atoms
H-Ar.
On-line manual is available at this web site.
You can also download the source code of psi88 from
the above site as a ``psi88.tar.gz''. When you do ungzip and
untar this archive, you will obtain some documents and
the ``psi88.tar.Z'' file which is required at this port.
"The SEQIO package is a set of C functions which can read and write
biological sequence files formatted using various file formats and which
can be used to perform database searches on biological databases."
- from the README file
A suite of tools for visualising sequence alignments.
Blixem is an interactive browser of pairwise alignments that have
been stacked up in a "master-slave" multiple alignment; it is not
a 'true' multiple alignment but a 'one-to-many' alignment.
Belvu is a multiple sequence alignment viewer and phylogenetic tool.
It has an extensive set of user-configurable modes to color residues
by conservation or by residue type, and some basic alignment editing
capabilities.
Dotter is a graphical dot-matrix program for detailed comparison
of two sequences. Every residue in one sequence is compared to every
residue in the other, with one sequence plotted on the x-axis and
the other on the y-axis.
SSAHA is a software tool for very fast matching and alignment of DNA
sequences. It stands for Sequence Search and Alignment by Hashing
Algorithm. It achieves its fast search speed by converting sequence
information into a `hash table' data structure, which can then be
searched very rapidly for matches.
SSAHA: a fast search method for large DNA databases (2001).
Ning Z, Cox AJ, Mullikin JC. Genome Res. 11: 1725-9.
PMID: 11591649
BasicDSP is an educational tool that makes it easy to experiment with simple
Digital Signal Processing algorithms for audio signals. The input can either
be taken from the sound card, or be a locally generated sine wave, white noise
or impulse signal. The output is fed to the sound card, as well as to a virtual
oscilloscope and spectrum analyzer.
Electric is a sophisticated electrical CAD system that can handle
many forms of circuit design, including:
Custom IC layout (ASICs)
Schematic drawing
Hardware description language specifications
Electro-mechanical hybrid layout
(snip, this is an edited version of Electric's homepage)
Electric handles these file formats:
CIF I/O
GDS I/O
VHDL I/O
DXF I/O
PostScript, HPGL, and QuickDraw output
For real functionality, one should consider installing
support simulation software such as cad/spice.
FEAPpv is a general purpose finite element analysis program which is
designed for research and educational use. The program is described in the
references:
The Finite Element Method, 6th ed., Vols. 1 and 2, by O.C. Zienkiewicz and
R.L. Taylor, Elsevier, Oxford, 2005.
FEAPpv is designed to be compatible for compilation in Unix/Linux and
Windows PC environments.
No support on use of the program will be provided.
gSpiceUI is intended to provide a GUI for freely available electronic
circuit simulation engines ie. NG-Spice and GNU-Cap. The utility gnetlist is
used to convert schematic files to netlist files, Gwave or Gaw to display
simulation results and gschem is the preferred schematic capture tool.
SPICE is a general-purpose circuit simulation program for nonlinear DC,
nonlinear transient, and linear AC analyses. Circuits may contain resistors,
capacitors, inductors, mutual inductors, independent voltage and current
sources, four types of dependent sources, lossless and lossy transmission
lines (two separate implementations), switches, uniform distributed RC
lines, and the five most common semiconductor devices: diodes, BJTs, JFETs,
MESFETs, and MOSFETs.
Patch Levels I and II (including a new spec command for spectral analysis)
and the level 2 JFET model are courtesy from the Macquarie University.
Online documentation at: