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University of Wyoming

Welcome to The Adaptive Evolution Database

The Liberles lab is currently moving to Temple University. As a result all data on this website will be temporarily unavailable. The content will be restored in November, 2014.

, the TAED database currently viewable on this version of the website is not complete. It will be updated as more data becomes available.

SPECIAL NOTE: As of the data currently present on the website is old data that will be replaced by more refined data when the improved data becomes avaliable.

Objectives and Goals of TAED

When complete, TAED will allow users to investigate sets of candidate genes under positive selection along each lineage of the NCBI taxonomy within Chordates, as well as tracing gene duplication events that mapped to each species tree lineage. In addition to the presentation of alignments and gene trees with lineage-specific dN/dS and information organized through the reference species tree, users will also be able to visualize pathways from KEGG that show multiple genes under positive selection in a particular lineage and automatically view generated homology models of structures from PDB (where available) with substitutions that occurred on lineages with dN/dS > 1 visualized.

The six primary functions are tabs across the top of each sceen within TAED.

TAED Introduction provides a brief background of the TAED development, references and overview of the database.

TreeThrasher is the 3d tree viewing software to visualizing all trees within TAED. From this tab, the user can read the TreeThrasher manual, peruse FAQs about TreeThrasher, and download the application. Users can visualize any tree in a Newick file format with TreeThrasher.

TAED Search allows the user to search using GI numbers, any portion of the protein name, or the genus and species name for gene family trees within TAED.

TAED BLAST allows the user to enter a protein sequence and do a BLAST search against the TAED.

Tree of Life is the Chordate species tree. The user can select to view the entire tree or only those species that have trees with a dN/dS value greater than 1 associated with them.

TAED Alphabetical Family Search allows the user to search TAED for gene families alphabetically.