McVicker G and Green P: Genomic signatures of germline gene expression. Genome Res 20:1503-11 (2010).

Background selection (B) value estimates calculated using gcons conserved segments
(score > 10) and a finescale recombination map (Myers et al. 2005). Coordinates are for the NCBI36/hg 18 version of the human genome assembly.

Reference:

McVicker G, Gordon D, Davis C, Green P: Widespread genomic signatures of natural selection in hominid evolution. PLoS Genetics 5(5): e1000471 (2009).

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Dick Hwang

AMBIORE - Applications for MCMC Bayesian Inference of Rates in Evolution.

This software implements a flexible and computationally efficient Bayesian Markov chain Monte Carlo approach to estimating rates in evolution given a sequence alignment and tree topology relating the species. The evolutionary model allows substitution rates at a site to depend on the two flanking nucleotides, the branch of the phylogenetic tree, and position within a sequence.

The package [220K] includes C source code and documentation.

Reference:

Hwang DG and Green P: Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proceedings of the National Academy of Sciences U.S.A. 101:13994-4001, Epub Aug. 03 (2004).

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Chris Saunders

CodeAxe -analysis of mutation and selection in coding sequence

CodeAxe is a tool for the phylogenetic analysis of mutation and selection in coding sequence. It provides approximate maximum likelihood nucleotide, codon and "extended codon" models that allow for neighbor-dependent nucleotide mutation, asymmetric exchange-dependent amino acid selection, nonreversible evolution and mixture models of mutation and selection classes.The method is described in:

Saunders CT and Green P: Insights from modeling protein evolution with context-dependent mutation and asymmetric amino acid selection. Molecular Biology and Evolution 24(12): 2632-47.

CodeAxe was developed by Chris Saunders and is licensed under the GNU GPL. Source code and usage examples are available in the following package:

CodeAxe-1.0.tar.bz2 [683K]

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DATA: Kavita Garg

We have formed 3077 donor and 4628 acceptor PAIRS of conserved constitutive and conserved alternative splice sites from the sam transcript for our analysis. We also created datasets of orthologous alternative and constitutive splice sites in mouse, rat and human.

Supplementary Table 3 download: S3

Supplementary Table 4 download: S4

Supplementary Table 5 download: S5

.