Phylogenetic Analysis with Space/Time Models


PHAST Resources


The core libraries for PHAST and several initial programs (including phyloFit, exoniphy, and phastCons) were developed between 2002 and 2004 as part of Adam Siepel's dissertation work in David Haussler's group at UC Santa Cruz.
Since that time, several new programs have been added, various improvements to the libraries have been made, and the user base has gradually expanded from a small group of close collaborators to several hundred people with diverse research interests.
In 2006 the project moved to Cornell. The project then moved to Cold Spring Harbor Laboratory in 2014.
From 2008 to 2014, Melissa Hubisz was the lead programmer working on PHAST and RPHAST and she still continues to be a a part of the Siepel Lab. Ritika Ramani is now the lab programmer working on PHAST and RPHAST.

PHAST development and maintenance is supported by NIH Grant R35 GM127070-01. Past funding sources have included the National Institute of Health (NIH), the National Science Foundation (NSF), a David and Lucile Packard Fellowship for Science and Engineerin, an Achievement Rewards for College Scientists (ARCS) scholarship, and a Graduate Research and Education in Adaptive bio-Technology (GREAT) fellowship from the University of California Biotechnology Research and Education Program (UCBREP).


A number of collaborators have helped to improve PHAST during the course of its development. In particular, Elliott Margulies (NHGRI) was a devoted and patient user early in the project, and his constructive feedback led to a number of new features, bug fixes, and other improvements. Valuable feedback has also come from Kate Rosenbloom and Hiram Clawson (UCSC), and James Taylor (previously Penn State, now Emory U.). Katie Pollard has contributed to the theory behind the dless and phyloP programs, and has also made many valuable suggestions for features and bug fixes.


From 2004-2007, PHAST was freely available for academic use, by email request, but the right to license it for a fee for commercial use had been reserved (at the advice of the UC administration). As of 2008, the package is fully open source, and is available for download from these pages under the terms of a BSD-style license.


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, Siepel A (2011) PHAST and RPHAST: Phylogenetic analysis with space/time models. Briefings in Bioinformatics 12:41–51.

Siepel A, Haussler D (2004) Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol Biol Evol 21:468–488.

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

Capra JA, Hubisz MJ, Kostka D, Pollard KS, Siepel A (2013) A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes. PLoS Genet 9:e1003684.

Siepel A, Haussler D (2005) Phylogenetic hidden Markov models. In: Nielsen R, editor, Statistical Methods in Molecular Evolution, New York: Springer. pp. 325–351.

Siepel A, Pollard K, Haussler D (2006) New methods for detecting lineage-specific selection. In: Proc. 10th Int’l Conf. on Research in Computational Molecular Biology. Berlin: Springer-Verlag, pp.190–205.

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

Siepel A, Haussler D (2004) Combining phylogenetic and hidden Markov models in biosequence analysis. J Comput Biol 11:413–428.

Siepel A, Haussler D (2004) Computational identification of evolutionarily conserved exons. In: Proc. 8th Int’l Conf. on Research in Computational Molecular Biology. New York, NY: ACM Press, pp. 177–186.