HYPHY Documentation.
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A brief guide to HyPhy
How to use HyPhy for sequence analysis shown through a collection of examples.
Batch Language Command Reference
A complete searchable database of HYPHYKernel batch commands, functions, operations etc (updated for current versions). Also see an
all-in-one PDF
.
Online
HYPHY
Tutorial
a good "Getting Started" reference, also available as a
PDF file
.
Standard Analyses
[This section is not current. Version 0.99 includes a host of new and improved analyses].
GUI Examples
Compilation Error Fixes
How to fix HyPhy source code if the compiler chokes [Applies to version 0.95; version 0.99 incorporates the fixes].
Methodology Overview
Stochastic Modeling of sequence evolution with Maximum Likelihood framework.
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002
