FAT-CAT: Fast Approximate Tree Classification
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The FAT-CAT webserver uses subtree HMM scoring to place user sequences into pre-calculated phylogenetic trees in PhyloFacts, from which orthologs are identified and function is predicted. Some results can take hours to complete; we recommend that you provide your email address or bookmark the results page.
About FAT-CAT | Pre-calculated results | Supplementary Materials
The stages of the FAT-CAT pipeline are described in detail here.
Stage 1 Parameters: Family HMM Searches
These parameters control the precision and recall of Stage 1 family HMM searches.
Fraction of the query that matches an HMM
Fraction of the HMM that matches the query
Stage 2 Parameters: Subtree HMM scoring and phylogenetic placement
These parameters control the precision and recall of Stage 2 subtree HMM searches and the definition of the Enclosing Clade of presumed orthologs.
Stage 2.3: Subtree HMM alignment evaluation (between the query and the TSN HMM)
Fraction of the query that matches an HMM
Fraction of the HMM that matches the query
Stage 2.4.1: Tolerated divergence among sequences in the TSN
Stage 2.4.2: Enclosing Clade Criteria
Expand the TSN to the largest Enclosing Clade supported by orthology methods selected below.
For highest precision, check all orthology methods, and require all to support an Enclosing Clade.
For highest recall, check all orthology methods, and require 1 to support an Enclosing Clade.
Require any of the following orthology method(s) to support an Enclosing Clade:
, threshold:
% identity
Stage 3 Parameters: Ortholog Selection
Adjust these parameters to modify which sequences are considered orthologs to your query.