Making your own copy of the course workstation

... and some other software you might find useful

Instructions (in Czech) and files for setting up the real course workstation are here.

Color key:

All programs downloadable from here are either freeware, free for educational/home use or free demo/trial versions.

Clustal W/ Clustal X

Clustal W is a standard multiple alignment program, written originally for Unix and even for VMS (anyone remembers that?), so lots of non-Windows versions are available.Clustal X, though, is a Win-specific graphical interface. Both can be obtained here.

Reference: Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22):4673-4680.

MACAW (Multiple Alignment Construction and Analysis Workbench) by S. Altschul et al.

- old but good, runs on anything from 386 with Win 3.1 upwards! No longer supported by NCBI where it was developed, but still around in the Net. Download here from the author´s ftp site (209 kB) and unzip to a folder on your disk (it just resides in its own folder without affecting the Windows registry). A Mac version exists as well.

BioEdit

- an ever better free package for alignment editing, includes a CLUSTAL interface and a possibility to work with translated DNA, by Tom Hall, North Carolina State University.
Download from the author here. (The author´s site experienced some problems, and may still carry only old version. The recent version is mirrorred on my workstation setup page).

pDRAW32 by Kjeld Olesen

- a LOVELY plasmid-drawing and restriction analysis program. Technically not freeware but beerware, which means: if you meet the author, buy him a beer. If you feel that you are owing something to me, and if you happen to meet Kjeld Olesen, please invite him instead of me (just to increase the probablility :-)

The program gets updated fairly frequently, so it is best to download directly from the author:
http://www.acaclone.com

 

Note: we are all growing old, including the author, apparently! Thus, the program has been recently upgraded from beerware to shareware, but the unpaid version still works.

PlasmaDNA

- a bigger, better, smarter, completely free alternative to pDraw32. Also more complicated and somewhat less user-friendly. Available here.

PHYLIP - the classical phylogeny package by Joe Felsenstein

Visit the author's pages to get the newest version for your system. Ported from Unix, therefore likely to run better/faster on a Linux.

PHYML

A program to compute maximum likelihood trees by a fast heuristic method is available here for download. Compatible with PHYLIP.

TreeCon - phylogenetic tree construction by Yves Van de Peer

A faster and in some aspects simpler/smarter alternative to PHYLIP for construction of sequence-based trees. Available from the author's site (including manuals and a new patch).

Reference: Van de Peer Y, De Wachter R. (1994) TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Computer Applications in the Biosciences, 10: 569-570.

TreeView X- a nice utility for plotting trees by Rod Page

A good tool for displaying trees made by PHYLIP, Clustal and some other programs. Produces emf output that can be further edited in many graphics programs. Available from the author's site (including manuals).

DeepView (alias spdbv - the Swiss PDB Viewer)

Viewer for 3D structures with lots of extra functions, including modelling. Download the install here from the developers site, or from my local mirror (Windows version only). Available for multiple platforms.

The Sequence manipulation suite by Paul Stothard

This package will be used extensively throughout the course. Since it is javascript based, it is platform-independent and does not have to be on the workstations - the course work will be based on a server copy (you can link to it and try out here). If you want to have your own copy at home or at your department server, follow the instructions available from the left-hand menu of SMS.

Persistence of Vision Raytracer (PoVRay)

All you need for 3D visualisation of virtual scenes is available here. Warning: it can be addictive!