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HYPHY Package >> HyPhy feedback >> Documentation
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Message started by John Del Greco on Jul 15th, 2006 at 2:00pm

Title: Documentation
Post by John Del Greco on Jul 15th, 2006 at 2:00pm
What documentation is available for HyPhy?  In particular, are there Help files available with the software?  The only documentation that I have is:

(1)  HyPhy:  Hypothesis Testing Using Phylogenies
(2)  Maximum Likelihood Framework for Genetic Sequence Analysis
(3)  HyPhy Users Manual

Cheers,
John

Title: Re: Documentation
Post by Sergei on Jul 15th, 2006 at 6:15pm
Dear John,

HyPhy documentation is, sadly, lacking. The three items you list can also be supplemented with

1). Old (3 years out of date) standard analyses documentation Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login These files are also in the Help directory of the HyPhy distribution.

2). Some simple GUI examples Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login

3). Example batch files in the 'Examples' directory of the distribution (look at the comments embedded in the source for guidance).

4). HyPhy language command reference (about 6 months out of date, will be updated soon): Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login

If you have specific questions, it may be best to post them on this message board.

Cheers,
Sergei

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