The Tools used in Bioinformatics

NCBI Map Viewer
For finding genes and gene products (RNAs and proteins) that interest you
BLAST
For finding genes or proteins with sequences similar to yours
ClustalW
For comparing your sequence with others, and lots of sequences with each other
Phylip
For making phylogenetic trees, which show how sequences are related to each other.
Treeprint
For printing phylogenetic trees
PSIPRED
For predicting the location of helices, pleated sheets, and transmembrane elements of proteins of unknown structure
Swiss-Model
For automated building theoretical structural models of your sequence based on known structures (homology modeling)
Deep View (also knows as Swiss-PdbViewer)
For seeing and exploring macromolecular models in three dimensions, and for manual and semiautomated homology modeling
PubMed
For searching ALL the literature of the life sciences
ExPASy (Expert Protein Analysis System
Not so much a tool as a tool box -- a very complete set of protein analysis tools