Links to Molecular Biology and Other Things

Genome Projects and Databases

Sequence and Alignment tools:

The Biology Workbench: An integrated environment with many of the common sequence and alignment tools in one place and a reasonable friendly interface. Especially useful tools are the MSASHADE program for color coded plots of sequence alignments and translation and complement-generating programs for DNA sequences.
NCBI ( National Center for Biotechnology Information)

Entrez Sequence Database Search
BLAST Sequence similarity search

Baylor College Of Medicine Links

PAM and Blosum
A DNA sequence Translator
A Codon Usage Database
Another site for protein homology search by alignment
BOXSHADE Alignment Visualization Tool
European Bioinformatics Institute

Clustalw at EBI

Molecular Biology Methods and Resources

Phylogeny and Tree-building Pages:

Felsenstein's Phylogenetics Pages

Felsenstein's Phylip Package and links to other phylogeny packages

Another PHYLIP reference

Other Referenced Packages

PAUP* (Phylogenetic Analysis Using Parsimony (*And other methods) This is phylogeny package that I most commonly use.
PAML
Treeview is a nice package for visualizing and editting phylogenetic trees that produces high quality output.
The University of Arizona's Tree of Life Project

Genetics

Linkage Analysis

Journals and Reference