PhastWeb is an easy-to-use web application that will generate conservation-scores or predict conserved elements for a user-provided multiple sequence alignment using phastCons or phyloP.
PhastWeb can either use a neutral phylogenetic model provided by the user, or it can estimate a crude model from the provided sequence alignment. A model can be estimated either using a provided tree topology or one estimated by neighbor-joining.
Run times are estimated based on the size of the alignment and the number of species. Jobs will be rejected if their estimated runtime exceeds 24 hrs. For estimated run times please refer to this graph.
Users can immediately visualize conservation scores using the UCSC Genome Browser track hub. In addition, all files generated by PHAST can be downloaded for further analysis (files are deleted from our server after 7 days).