Softwares for Bioinformatics

FTP
Netterm
WebLab Viewer
gstools
Mage
plasmid processor 1.02
Prekin
Primer
Promsed
RasMol
Biowire-Jellyfish
Swiss-Pdb Viewer
Sequin95

Vector NTI
X-Win412
Winseq
Winplasd


Chromas: Trace file viewer 
[Download
[Help]


SeqVerter:
 
Free sequence file format conversion 
[Download
[Tutorial]

Octopus 
is an easy-to-use graphical user interface designed for the rapid interpretation of BLAST, BLAST-2 and FASTA output text files.
[Download]

SEQtools is a comprehensive program package for handling and analysis of  nucleotide and protein sequences. The program includes a series of trivial functions to help you carry out common operations.

Special functions are included for design of microarray gene expression analysis experiments, for expression analyses with the SAGE procedure and for managing small EST projects. Utilities are  included for primer design and ordering, renaming files, creating codon usage tables, building local searchable databases, aligning nucleotide and protein sequences, comparing sequences and a lot more...
[Registration]


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BioEdit is a biological sequence alignment editor written for Windows 95/98/NT.  A rich, intuitive multiple document interface with many convenient features  makes alignment, manipulation and viewing of sequences relatively quick and easy on your desktop computer.    Several sequence manipulation and analysis options and fully-automated links to local and WWW-based anaylsis programs facilitate an integrated working environment which allows you to view, align and analyze sequences from a single application with simple point-and-click operations. [Download] [Manual]


PHYLOGENETICS
[PHYLIP logo here]PHYLIP is a free package of programs for inferring phylogenies. It is distributed as source code, documentation files, and a number of different types of executables.  http://evolution.genetics.washington.edu/phylip.html
  Download phylip V3.5

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GENDOC is a Full Featured Multiple Sequence Alignment Editor, Analyser and Shading Utility for Windows. Features includes: Data Analysis and Visualization, Score assisted manual alignment, Paginated Printouts, Windows Based, Highly Configurable, Exported Figures and Phylogenetic Tree support.   http://www.psc.edu/biomed/genedoc/
  Download Gendoc V322700 (March, 2007)

TREEVIEW is a program for displaying and printing phylogenies. The program reads most NEXUS tree files (such as those produced by PAUP and COMPONENT) and PHYLIP style tree files (including those produced by fastDNAml and CLUSTALW).
http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
  Download Treeview V1.6.6 (Sep, 2001)


Software and Databases for Computational Biology on the Internet


This page is a supplement to the book Computational Methods in Molecular Biology, edited by Steven Salzberg, David Searls, and Simon Kasif. The publisher is Elsevier Sciences. Please contact Steven Salzberg (salzberg@cs.jhu.edu) if you wish to have your software referenced on this site, or if you wish to change the description of your software already listed here.


Gene finders and other sequence analysis programs