Type in a rooted ultrametric tree (Newick format only)
Type in a multiple sequence alignment (MSA) (FASTA format only)
Type: DNA Protein
Type in trait binary states (FASTA format only)
Optional input - protein structure
Using this option projects the TraitRateProp site predictions on the PDB structure
Provide a PDB format file or ID and a chain ID
Each structure in the PDB is represented by a 4 character alphanumeric identifier.
Each chain ID is a single alphanumeric identifier.
For more details, see the PDB website
Optimize p - site proportion parameter
The TraitRateProp alternative model optimizes the parameter p - proportion of sites in association with the phenotypic trait.
If you choose not to optimize the proportion parameter, its value [0,1] should be provided. Notably, if p is not optimized and set to 1, the run is equivalent to the TraitRate alternative model.
Range of rate ratio parameter for starting points
The r values for the starting points are sampled between 1/r_max and r_max. The value of r_max should be > 1.Here we also limit it to be < 10.
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Job title (optional)
Enter a descriptive job title for your TraitRateProp query