Modelling protein evolution

Update: 2011-06-27

Description

I'll describe our recent efforts to model protein evolution and amino-acid substitutions by (1) designing an easy to use pipeline to estimate amino-acid replacement matrices for specific protein groups, (2) using the protein structure, (3) simplifying mixture models that have been proposed so far. I'll discuss several issues related to models (e.g. complexity trade-off), biology (e.g. independence of nucleotide mutations) and theory (e.g. identifiability, prediction of ancestral sequences).

Comments

In Channel

Estimating ultra-large phylogenies and alignments

2011-06-2856:13

The combinatorics of distance-based tree inference

2011-06-2817:50

Assessing the limits of phylogenomics: can too much data be a bad thing?

2011-06-2701:04:29

Stochastic Errors vs. Modeling Errors in Distance Based Phylogenetic Reconstructions

2011-06-2720:34

Integrative analysis if environmental sequences

2011-06-2701:00:47

Mammalian phylogeny reveals recent diversi cation rate shifts

2011-06-2725:01

A generalization of Stirling numbers and distribution of phylogenetic trees

2011-06-2717:17

A Lie algebraic classification of continuous-time Markov models

2011-06-2722:34

Tree reconciliations: beyond the LCA mapping

2011-06-2719:06

Coalescent-based Species Tree Inference from Gene Tree Topologies Under Incomplete Lineage Sorting by Maximum Likelihood

2011-06-2717:54

Speciation & Extinction Rate Estimation from Phylogenetic Trees

2011-06-2722:15

Trees as representations of evolutionary information worth keeping

2011-06-2759:54

Are there alternatives to handling site-to-site rate variation in evolutionary characters

2011-06-2701:06:53

An empirical study of the effect of sequence alignment on phylogenetic analysis

2011-06-2720:41

Modelling protein evolution

2011-06-2757:39

Sequence Classification using Reference Taxonomies

2011-06-2401:03:44

Evaluating the goodness of fit between a phylogenetic model and an alignment

2011-06-2457:49

Phylodynamic inference - accounting for the interaction of evolutionary and ecological processes

2011-06-2415:40

Genome sequencing of Leishmania donovani clinical lines reveals dynamic phylogenetic variation

2011-06-2421:10

New methods of identifying fast-evolving sites in aligned sequence data

2011-06-2424:42

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Modelling protein evolution

#box-pro-ellipsis-175770533665975{-webkit-line-clamp:2;}Modelling protein evolution

Modelling protein evolution

Steve Greenham

Modelling protein evolution