Web-interactive services

Primer Design
    Primer3 (Whitehead Inst, MIT)
    CODEHOP (Degenerate primers)

ClustalW Multiple sequence alignment

Software Sites

BIMAS - BioInformatics & Molecular Analysis Section, NIH
bioinformatics.org - The Open Lab
bio.perl.org - Perl bioinformatics library
Debian Packages in Biology
ExPASy Tools Proteomics tools
GeneMark - Gene Prediction program of Mark Borodovsky
Linux binaries for Biology
NCBI - National Center for Biotechnology Information
openscience.org - Open Source software for the sciences
SAL - Scientific Applications on Linux
TIGR Software - packages from The Institute for Genomic Research
Virtual Genome Center at the University of Minnesota Medical School
www.phrap.org - U. of Washington (phred, phrap, consed, swat, RepeatMasker)
In Silico - simulation of molecular biology experiments

Programs and Packages

Sequence Comparison

Blast - NCBI's sequence similarity search tool (tutorial    course)
FASTA - Sequence comparison program (UVA)

Multiple Alignment

Tcoffee
ClustalW and ClustalX - Multiple Sequence alignment program

Gene Prediction

Glimmer - TIGR's gene-finding program
MAGPIE - Automated Genome Project Investigation Environment

Software Suites

ACEDB
bioTk
NCBI Tools - vibrant, asn, etc
EMBOSS - European Molecular Biology Open Software Suite

Phylogenetic trees

PHYLIP - programs for inferring phylogenies

Miscellany

BCM Trace Viewer (Java)
MolScript - 3D Protein display package
PolyPhred - SNP analysis with U. Washington software

Data Formats

mmCIF - mmCIF page at Rutgers