Information, documentation, and news about the HyPhy software package. HyPhy Hypothesis Testing using Phylogenies. HyPhy. Home News and Releases About Installation Getting Started Methods Selection Tutorials. CLI Tutorial CL Prompt Tutorial Batch Language. Reference Library ...

HyPhy distributes a variety of methods for inferring the strength of natural selection in your data using, in the case of codon-based methods, the dN/dS metric. Here, we provide an overview of each method.

Using HyPhy-GUI to detect selection. These tutorials outline how to use the HyPhy Graphical User Interface (GUI) desktop application (HyPhy-GUI) to detect natural selection in protein-coding alignments.

To download the Desktop/GUI version of HyPhy, follow instructions on this download page. NOTE: The HyPhy GUI is no longer maintained and will be replaced in the near future with a JavaScript front-end.

to use HyPhy for simple model fitting, we will introduce the fundamental components required of virtually every HyPhy data analysis. 1. Data Set. A Data Set is a multiple sequence alignment. HyPhy is able to read a variety of sequence formats, including as NEXUS, PHYLIP and FASTA. 2. Data Filter. A Data Filter specifies a part (or parts) of a ...

HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning. It features a rich scripting language for limitless customization of analyses.

Video tutorials for DataMonkey.org and HyPhy; Using HyPhy as a Command Line Tool; Using HyPhy Interactive Command Line Prompt to Detect Selection; Using HyPhy-GUI to Detect Selection; Labeling branches with phylotree

HyPhy provides a suite of diverse phylogenetic methodologies for testing specific hypotheses about the selection in protein-coding and/or amino-acid multiple sequence alignments. Which method you select will depend on your specific question.

MPI - build a HyPhy executable (HYPHYMPI) using the message passing interface MPI to support parallel execution on distributed systems (clusters). An MPI library (e.g., OpenMPI) must be installed and available in your path.

Through the HyPhy command-line, see above for the HBL implementation Through our BUSTED ModelTesting procedure, see above and our dedicated repository for details. Vizualizations / Interactive Notebooks