TraitRateProp Logo Detecting trait-dependent
evolutionary rate shifts
in sequence sites

Prof. Itay Mayrose Lab - Plant Evolution, bioinformatics, & comparative genomics
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Type in a rooted ultrametric tree (Newick format only)

A species tree, where the distance from each tip to the root is the same. The root node has exactly 2 children.


or upload file (Newick format only)                                                                          


Type in a multiple sequence alignment (MSA) (FASTA format only)                Type: DNA   Protein


or upload file (FASTA format only)                                                                            


Type in trait binary states (FASTA format only)

Each taxon in the tree (and MSA) has one of two trait states ("1" or "0")


or upload file (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


    Enter a PDB ID:     or  upload file
        and enter a chain ID:  
        and the name of the reference sequence:  



(+) Advanced

Optimize p - site proportion parameter                        Yes   No   

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.

Enter p:  

Range of rate ratio parameter for starting points      r_max:     

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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