La Folie, Quo Vadis, Evo-Devo?

ProPhylER

http://www.prophyler.org/index.html

ProPhylER provides predictive evolutionary analyses of eukaryotic proteins.

ProPhylER puts comprehensive constraint data on tens of thousands of eukaryotic proteins, represented by hundreds of thousands of individual sequences, at the fingertips of the researcher.

PHAST is a freely available software package for comparative and evolutionary genomics.

Rate4Site

Rate4Site is a program for detecting conserved amino-acid sites by computing the relative evolutionary rate for each site in the multiple sequence alignment (MSA).

Genomic Evolutionary Rate Profiling: GERP

GERP identifies constrained elements in multiple alignments by quantifying substitution deficits.

These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint.

We refer to these deficits as "Rejected Substitutions".

Rejected substitutions are a natural measure of constraint that reflects the strength of past purifying selection on the element.

GERP estimates constraint for each alignment column; elements are identified as excess aggregations of constrained columns.

A false-positive rate (which is user-settable) is calculated using 'shuffled' alignments in which the order of columns is randomized.