DNA/MOLECULAR BIOLOGY TOOLS:

The following is a list of some of the sites related to DNA applications that I have found useful at one time or another. If you think I am missing a key site(s), please let me know. Enjoy!

Primary:

• The National Center for Biotechnology Information

DNA Sequence Alignments:

• Blast (Part of the NCBI website; Primarily intended for sequence searches but also allows you to align two sequences).
• BCM Search Launcher: Multiple Sequence Alignments
• Clustal W - Japan (Provides PHYLIP ouput option).

DNA Sequence Editors/Chromatogram-DNA Visualization:

• BioEdit - Nice program for editing DNA sequences
• Chromas Lite - Program for editing DNA sequence chromatograms
• SeqVis - Alignment visualization tool

Primer Design/PCR tips:

• BioMath Calculator
• GeneFisher Primer Design
• PCR- Information on PCR
• PCRLinks.com
• Web Primer

Restriction Enzymes/Digestion Predictions:

• REBASE: The Restriction Enzyme Database
• Webcutter

Phylogenetics/Population Genetics Software:

• Arlequin 3.11 - Comprehensive population genetics software
• BAPS- Bayesian Analysis of Population Structure
• BEAST- Bayesian Evolutionary Analysis Sampling Trees
• BIMr- Bayesian Inference of Immigration Rates
• DAMBE
• FSTAT
• Genepop - Vey nice web program for basic population genetics analysis
• MANTiS
• Mark Miller's Analytical Software Package
• Microsat
• MrBayes: Bayesian Inference of Phylogeny
• PHYLIP (Phylogenetics Inference Package) - Powerful phylogenetics package
• Joe Felsenstein's List of Phylogenetics Software
• MEGA 4 - Very nice and user friendly phylogenetics software
• PASSaGE - Software for geographical genetics and spatial analysis
• TreeRot
• Structure - Powerful software for determing population structure

Microsatellite Scoring Tools:

• GeneScanView - Nice little shareware program for scoring micrsatellites

DNA Sequencing/Microsatellite Scoring Facilities:

• MEAD (Molecular Evolution of Adaptation and Diversity) EE SUNY Stony Brook
• University of Arizona Fragment Analysis Facility
• Davis Sequencing Facility
• SUNY Stony Brook DNA Sequencing Facility
• The University of Maine- DNA Core Sequencing Facility

Useful Commercial Sites:

• New England Biolabs- Site I use for restriction enzymes.
• Applied Biosystems - Sells fluorescent primers for genotyping.