Cote Laboratory
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    • Cyclic nucleotides as second messengers
    • The PDE superfamily
    • Central role of PDE6 during visual signaling
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Phylogenetics

There are four major methods for constructing phylogenetic trees, and no one approach is clearly preferred in all instances: (1) Distance (including neighbor-joining), (2) maximum parsimony, (3) maximum likelihood, and (4) Bayesian inference.
Regardless of the method, bootstrapping analysis should be performed to assess the robustness of the tree topology.

Tree-building Programs

Seaview performs multiple sequence alignments and can generate the following types of trees (all with bootstrapping analysis): (1) Distance (NJ or BioNJ with options); (2) Parsimony (PHYLIP, using the protpars algorithm); (3) Maximum likelihood (PhyML, with multiple options) 
MegAlign Pro (Lasergene) uses the BioNJ distance method to create the tree.
Jalview uses distance methods (including neighbor-joining) to create trees
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