HyPhy - Hypothesis Testing using Phylogenies - Information ...
HyPhy. Home News and Releases About Download Installation Getting Started Methods Tutorials Batch Language Resources Hypothesis Testing using Phylogenies An open-source software package. for comparative sequence analysis. using stochastic evolutionary models. Download. HyPhy News. HyPhy is ...
HyPhy - Hypothesis Testing using Phylogenies - Information ...
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.
HyPhy - Hypothesis Testing using Phylogenies - Information ...
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.
HyPhy - Hypothesis Testing using Phylogenies - Information ...
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.
HyPhy - Hypothesis Testing using Phylogenies - Information ...
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.
HyPhy - Hypothesis Testing using Phylogenies - Information ...
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 - Hypothesis Testing using Phylogenies - Information ...
Information, documentation, and news about the HyPhy software package. HyPhy Hypothesis Testing using Phylogenies. HyPhy. Home News and Releases About Download Installation Getting Started Methods Tutorials Batch Language Resources Methods# General Information; Selection; Stand Alone Analyses ...
HyPhy - Hypothesis Testing using Phylogenies - Information ...
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.
HyPhy - Hypothesis Testing using Phylogenies - Information ...
Tutorials for using standard methods in HyPhy to infer selection ware available here. Detailed descriptions of these methods are available here. Current HyPhy selection analyses output JSON-formatted files, whose contents are documented here. Book chapters and Powerpoints detailing HyPhy usage: Quantifying Natural Selection in Coding Sequences ...
HyPhy - Hypothesis Testing using Phylogenies - Information ...
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