Various Epigenetics resources listed through Epigenie
Galaxy–For analyzing genomic data. Awesome resource.
SeqDoc–Sequencing chromatogram analyzer useful for searching for mutations. Compares test sequences against a reference sequence of yours and produces a visual display of specific nucleotide differences
Human Splicing Finder–Program that can analyze intronic and exonic sequence mutations and produce percent-wise results of how certain splice sites would be theoretically affected by the mutations.
UCSC Genome Browser–The gold-standard for finding gene and transcript sequences, reported SNPs and gene location.
BLASTn–Using FASTA format nucleotide sequences, analyzes the similarity of the sequence to the reference genome.
Primer 3–Non-pyrosequencing primer design. Quick and easy.
Bisearch–Electronic-PCR. Anneals designed Pyro primer sequences to a bisulfite converted reference genome.
Reverse Complement Generator–Generates the reverse complement of any nucleotide sequence, useful for finding sequences in Word or other text programs.
OMIM–Human disease/mutation info associated with any gene
Vassarstats–quick and easy stats