From HyPhy Wiki
This page lists some user guides and book chapters that we have written on using HyPhy.
- Datamonkey - A tutorial on using the online version of HyPhy.
- Selection Analyses - A tutorial on selection analyses that was prepared for the Vancouver 2011 Workshop.
- Compartmentalization - From the same workshop, a tutorial on using HyPhy to detect compartmentalization.
- A tutorial on compartmentalization analyses (PDF)
- Ultradeep Sequence Analysis Pipeline for HIV-1
- GpGPU adaptation of the likelihood computing engine
- SLK Pond, B Murrell, and AFY Poon. Evolution of viral genomes – interplay between selection, recombination and other forces. In Evolutionary Genomics: Statistical and Computational Methods. Edited by Maria Anisimova. Humana Press; 2012 edition (March 14, 2012) Download PDF
- SLK Pond, AFY Poon, and SDW Frost. Estimating selection pressures on alignments of coding sequences. In The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing. Edited by Philippe Lemey, Marco Salemi and Anne-Mieke Vandamme. Cambridge University Press, 2009. Download PDF
- AFY Poon, SDW Frost, and SLK Pond. Detecting selection in DNA sequences with Datamonkey. In Bioinformatics for DNA Sequence Analysis (Methods in Molecular Biology vol. 537). Edited by David Posada. Humana Press, 2009. Download PDF
- Sergei L. Kosakovsky Pond and Spencer V. Muse. 2005. HyPhy: Hypothesis Testing Using Phylogenies. In Statistical Methods for Molecular Evolution. Statistics for Biology and Health, 2005, Part II, 125-181. Download PDF