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Data Analysis and Processing Guide

The document discusses the development of a HETEROGENEOUS model in a Bayesian framework to address the limitations of the homogeneity hypothesis in nucleotide frequency analysis. It highlights the discrepancies observed in real data sets and the implementation of a heterogeneous rooted tree in the PHASE software, which allows for variation in substitution models across different branches. Additionally, it provides guidance on using MCMC chains and constraining parameters within the model for accurate phylogenetic analysis.

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Michael Panelo
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7 views2 pages

Data Analysis and Processing Guide

The document discusses the development of a HETEROGENEOUS model in a Bayesian framework to address the limitations of the homogeneity hypothesis in nucleotide frequency analysis. It highlights the discrepancies observed in real data sets and the implementation of a heterogeneous rooted tree in the PHASE software, which allows for variation in substitution models across different branches. Additionally, it provides guidance on using MCMC chains and constraining parameters within the model for accurate phylogenetic analysis.

Uploaded by

Michael Panelo
Copyright
© Attribution Non-Commercial (BY-NC)
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd

Don Mariano Marcos Memorial State University South La Union Campus COLLEGE OF COMPUTER SCIENCE Agoo, La Union

SIMULATION AND MODELING ACTIVITY

Presented to:

Mr. Alfred Riloraza

Presented by:

Michael Panelo Paulo James Isidro Joy- Anne Boadilla

January 6, 2012 Date Presented

The HETEROGENEOUS model The homogeneity hypothesis implies that the substitution process ultimately reaches an equilibrium and it is also assumed that the process was already stationary at the very beginning, i.e., at the root of the phylogeny. If the homogeneity and stationarity assumptions were true, equal nucleotide frequencies would be expected in past and present-day sequences. Actually, we can observe discrepancy's in nucleotide frequencies in many real data sets of present species: model assumptions are clearly violated when using real sequences. It has been noticed that sequences of similar composition tend to be grouped together irrespective of their real phylogenetic relationships (Lockhart et al., 1994; Tarrio et al., 2001, see e.g., ). In an attempt to avoid this bias, we developed an HETEROGENEOUS model in a Bayesian framework which models coarsely the heterogeneity using a small pool of homogeneous processes. Each branch of the tree ``chooses'' a substitution model among them. The likelihood computation now depends on the position of the root which is why a heterogeneous rooted tree was implemented in PHASE (ultrametricity is optional). The composition observed at this root becomes a free parameter of the model (see, e.g., Yang and Roberts, 1995; Galtier and Gouy, 1998). Algorithms developed in PHASE are very similar to those implemented in P4 by Peter Foster. PHASE framework might be a bit more general since the full substitution model is allowed vary over the tree. However, you are strongly advised to limit yourself to variation of the composition vector as Foster (2004) did. Unfortunately, we did not have time to implement a way to use a single exchangeability matrix over the whole tree yet. There is a workaround (a bit unsatisfactory): you can start the MCMC chain from a model properly initialized and turn off the perturbation of rate ratios so that they have constant values. Use the same trick to fix the gamma shape parameter and the proportion of invariant sites to a single constant value. (Do not use a +I model with HETEROGENEOUS without constraining the proportion of invariant sites to a constant value). PHASE is missing an efficient MCMC proposal to modify the position of the root. You are advised to use an outgroup in the TREE block to constrain the position of the common ancestor. Remember that this outgroup can also be a monophyletic cluster. Source: [Link]

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