Welcome, Guest. Please Login
YaBB - Yet another Bulletin Board
 
  HomeHelpSearchLogin  
 
inferring topologies (Read 464 times)
konrad
Junior Member
**
Offline


I love YaBB 1G - SP1!

Posts: 53
inferring topologies
Oct 21st, 2005 at 8:46am
 
Hi Sergei,

The GUI allows me to infer tree topologies under a variety of nucleotide models, using neighbour-joining or maximum likelihood with different search techniques. How do I do these using batch files? (It looks like TopologySearch.bf does exhaustive search only; SingleBreakPointRecomb.bf seems to do neighbour-joining - is that right, and which parts of this file do I need for this? Simply copying the functions TreeMatrix2TreeString, ComputeDistanceFormula and InferTreeTopology into my file is not enough.)

Also, is it possible to infer ML trees using codon models, or is this just a bad idea due to excessive computational requirements?

thanks,
Konrad
Back to top
 
WWW WWW  
IP Logged
 
Sergei
YaBB Administrator
*****
Offline


Datamonkeys are forever...

Posts: 1658
UCSD
Gender: male
Re: inferring topologies
Reply #1 - Oct 21st, 2005 at 3:50pm
 
Dear Conrad,

First, a disclaimer. HyPhy was not intended to be a fast topology inference package (the exception is NJ, which is fairly quick). You can do some topology inference with codon models; I would recommend getting a starting NJ tree and then branch swapping (using TopologyInference:BranchSwap.bf), preferrably on a cluster.

To answer your question about including NJ code into your analysis: look at the NeighborJoining.bf in TemplateBatchFiles and, specifically at the InferTreeTopology function for the general case (which prompts for models and such). This function depends on the data being in the [bf]ds[/bf] dataset object and functions in distanceMethodNPBootstrap.bf.

The minimalist function for using NJ (based on SingleBreakPointRecomb.bf) will need to include the following functions:

InitializeDistances
ComputeDistanceFormula
TreeMatrix2TreeString
InferTreeTopology

The sequence of calls to build a tree would be

[code]
DataSetFilter filteredData = CreateFilter ... /* make your filter */
InferTreeTopology (0); /* do NJ and return internal tree representation */
treeString=TreeMatrix2TreeString(0); /* convert to string */
Tree givenTree = treeString; /* build a tree object */
[/code]

HTH,
Sergei
Back to top
 

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego
WWW WWW  
IP Logged
 
konrad
Junior Member
**
Offline


I love YaBB 1G - SP1!

Posts: 53
Re: inferring topologies
Reply #2 - Oct 24th, 2005 at 7:26am
 
Thanks! This works now.
Back to top
 
WWW WWW  
IP Logged