These pages are primarily intended for people just starting work in the Farrell lab and merely represent the approaches we use. However, they may be useful for other groups, especially the section on phylogenetic analysis.

PCR
List of primers used in the lab
Ordering and resuspending primers
Programs useful for PCR
Agarose gel preparation
Spin purification

Sequencing
Precipitation of sequencing reactions

Sequence editing and alignment
We use Sequencher 4.1 for sequence editing and ClustalX for alignment of difficult sequences (such as ribosomal DNA)
Trimming raw sequence
Labeling features (like introns)
Exporting sequences
Alignment parameters for Clustal
Profile alignments
Choosing the best alignment
Exclude hypervariable regions?

Phylogenetic analysis
Each item includes PAUP batch files or commands where appropriate. This is not an exhaustive manual, nor are the techniques original. These are just some of approaches which our lab has found generally useful. Some useful references which provide broader overviews are Phylogenetic Trees Made Easy by Barry Hall, Molecular Systematics, 2nd Edition,(chapters 11 and 12) edited by David Hillis, Craig Moritz, and Barbara Mable, and the recently updated Molecular Systematics website. PAUP also has a quick start tutorial on its web page. This page was last updated on December 12, 2007 , though most of its information has not been updated since June 10, 2002.

Step-by-step flow chart
Flow chart of strategies for phylogenetic analysis

Each step listed individually
NEXUS file preparation
Batch files
Testing for homogeneity, what to do if this fails
Saturation plots and weighting
Exhaustive and branch-and-bound searches (<13 taxa)
Heuristic searches
Parsimony ratchet
Bootstrap searches
Decay indices, including partitioned Bremer support
Choosing a likelihood model
Testing for a molecular clock
Calibrating using a published calibration
Calibrating using fossil data
Computing error bars on node times
Bayesian searches (MrBayes)
Hypothesis testing
Tree drawing and editing