HyPhy message board - SOWH test with multiple data partitions

	Welcome, Guest. Please Login

Home

Help

HyPhy message board › HYPHY Package › HyPhy feedback › SOWH test with multiple data partitions

(Moderators: Sergei, Simon)

‹ Previous Topic | Next Topic ›

Pages: 1

Send Topic

SOWH test with multiple data partitions (Read 2093 times)

Mariana Mateos

YaBB Newbies

Offline

Feed your monkey!

Posts: 1

SOWH test with multiple data partitions
Jun 17^th, 2009 at 9:37am

I usually perform my parametric bootstrap (SOWH test) with SeqGen. However, I would like to simulate my data under a more complex model than what is available in SeqGen. I'd like to have multiple partitions (codon positions 1, 2,3 and or genes). I'd like each to have a different model (e.g., codon position 1: HKY; codon position 2: GTR + G; etc.). SeqGen only allows gamma, gamma + invar sites, or site specific overall substitution rates, but not site-specific rate matrices, base freq, gamma, etc) Is this possible to implement in HyPhy? If so, is there a guide available?

IP Logged

wayne

Global Moderator

Offline

I love YaBB 1G - SP1!

Posts: 57
San Diego, CA
Gender: male

Re: SOWH test with multiple data partitions
Reply #1 - Jun 17^th, 2009 at 12:02pm

Hi Mariana, yes it will be possible to implement this using the HyPhy batch language. Have you used the batch language? The simulation setup should be rather trivial to setup. You can have a look at Chapter 5 of this file (Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

Login) which discusses filtering datasets by codon positions and applying separate models to each partition. Shout if you have questions. In the meantime we'll look into writing some "stock" code to run SOWH test. cheers ./w

ps: actually i think it may be possible to at least set up simulations in the gui. will look into this too.

Assistant Project Scientist&&Antiviral Research Center&&Department of Pathology&&University of California, San Diego

WWW

IP Logged

Pages: 1

Send Topic

‹ Previous Topic | Next Topic ›

« Home

‹ Board

Top of this page