HyPhy stands for "Hypothesis testing using Phylogenies". It is a software package that is designed around the fundamental objects of phylogenetics - the alignment, the tree, and the likelihood function. This design is based on the premise that any analysis of genetic sequences must take place within a phylogenetic framework because all sequences are the products of molecular evolution.
What can I do in HyPhy?
- Some of the more popular analyses in HyPhy include:
- Detection of natural selection (diversifying, purifying, or directional)
- Detection of recombination
- Detecting co-evolving residues in protein sequences
- Genomic and multiple-gene evolutionary inference
- Molecular clock and relative rate tests
- Nucleotide, protein and codon model selection
- As a likelihood analysis engine for other software and web services
Many of these popular analyses are also made available as web applications (Datamonkey), so that you can upload your data and select a method to run on our public high-performance computing cluster. With the batch language, the complexity of an analysis that you want to carry out on sequence data is essentially unlimited. (Or for practical purposes, limited by the power of your hardware and your patience!) In other words, you can implement a customized analysis, either by modifying one of the template batch files that are distributed along with HyPhy, or by writing one from scratch.
Hi Istvan,
I have to do selection analysis on few gene families from different species. I am confused whether to use codeml or hyphy. Just read on some post hyphy suits more to population genetics dataset. Is this true?
Thanks, RT.
Here is the link to the post which states that hyphy is not efficient in case of species with large distance Best Practices/Softwares To Calculate Ka/Ks Ratio How true is it?
I must say I am sufficiently knowledgeable of the differences between these tools - perhaps you could post this as a new, separate question so that that others with more experience will notice it and could comment.
I have posted this as a new question 'Hyphy vs codeml'.