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This is a web-interface to PHAT. Phat is provided as a high-order search tool. It allows the user to filter the large number of trees to more manageable numbers for which manual examination becomes feasible by excluding those trees that do not conform to specified selection criteria.
For help on the PHAT options and query syntax, go HERE
NOTE:If you are using Internet Explorer you may have difficulties viewing the results. This page has been tested and works with any of the more W3C-standards-compliant browsers (such as Mozilla, Firefox, Opera or Safari (Mac)).

PHAT PARAMETERS
Exclude the following taxonomic identifiers from the analysis (sequences will be treated as absent) ("Viruses, Viroids, other sequences, unclassified" would exclude all sequences belonging to these NCBI taxonomy groups) (!!!Case sensitive!!!)	Viruses, Viroids, other sequences, environmental samples, unclassified
Search for trees matching the following constraints: ("(Arabidopsis{=1}&Glycine max{=2})& !(*cellular organisms)" would return all trees containing a node in which one sequence of Arabidopsis is grouped together with two sequences of Glycine max and that node contains no other sequences belonging to cellular organisms)
Search for trees derived from chip:	ATH1-121501 Barley Citrus Cotton Grape Maize Medicago Poplar Rice Soybean Sugar_Cane Tomato
Minimum bootstrap support for nodes:(nodes with less bootstrap support are collapsed prior to analysis)
Checkquery (ensure the query sequence is part of the node corresponding to the selection criteria, otherwise discard tree):
Here you can specify various strings that will be searched for in the phylogenetic tree and highlighted by colors (yellow and red). (example: you use the Arabidopsis sequence identifier "261271_at" as a query, selected the Arabidopsis chip and want to have all Arabidopsis sequences in the tree colored in yellow and all sequences from Rice and Poplar colored in red (enter "Arabidopsis" in the right box and "Oryza ; Populus" in the left)).	RED: YELLOW:
Alternatively, enter the ID of a previously performed run (but make sure the parameters are still correct, i.e. the database and any species you want highlighted) The ID appears at the top of the results page (for example: "phatdPHnpe"). Results are stored for one week and can be accessed by specifying the job ID in this text field.