What's New

  • May 1, 2009. SiPhy version 0.5, the first publicly available version is now available.


SiPhy implements rigorous statistical tests to detect bases under selection from a multiple alignment data. It takes full advantage of deeply sequenced phylogenies to estimate both unlikely substitution patterns as well as slowdowns or accelerations in mutation rates.

It can be applied as an Hidden Markov Model (HMM), in sliding windows, or to specific regions. For more detailed information see documentation.

Getting Started

A quick tutorial to get you up and running.


Development of SiPhy is made possible by funding from the National Human Genome Research and the National Science Fundation.

nih nsf

SiPhy Data


To cite your use of SiPhy, please reference our publication Identifying novel constrained elements by exploiting biased substitution patterns, Bioinformatics 2009 25(12):i54-i62.


Available release.