phastWeb

Phylogenetic Analysis with Space/Time models (PHAST) is a freely available software package consisting of a collection of command-line programs and supporting libraries for comparative and evolutionary genomics. Best known as the search engine behind the Conservation tracks in the University of California, Santa Cruz (UCSC) Genome Browser, PHAST also includes several tools for phylogenetic modeling, functional element identification, as well as utilities for manipulating alignments, trees and genomic annotations.

The PHAST project was initiated by Principal Investigator, Adam Siepel with extensions by Melissa Hubisz.

The phastWeb application was developed by Ritika Ramani.

To download and learn more about PHAST please visit the PHAST Website.

The code is open source on Github.

Funding for PHAST including phastWeb is supported by NIH Grant R35 GM127070-01.

Ramani R, Krumholz K, Huang Y, Siepel A (2018) PhastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP. Bioinformatics, Volume 35, Issue 13, Pages 2320–2322

Hubisz MJ, Pollard KS, and Siepel A. 2011. PHAST and RPHAST: phylogenetic analysis with space/time models. Brief. Bioinform., 12 (1): 41–51.

Pollard KS, Hubisz MJ, Rosenbloom KR, and Siepel A. 2010. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res., 20: 110–121.

Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, et al. 2005. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res., 15 (8): 1034–1050.

For questions please contact phasthelp@cshl.edu.