Edit

Goldman Group

Evolutionary tools for genomic analysis

Empirical Codon Models

Our Empirical Codon Model (ECM) was published in 2007[1]. The following files were provided as Supplementary Material, originally appearing at http://www.ebi.ac.uk/goldman/ECM/ but no longer available from there.

MoreKappaModels.pdf

ECMrest.dat

ECMunrest.dat

ParameterValuesM0.txt

Table_lnL.txt

ProteinFamiliesSDT.txt

README

Definition of further kappa models

Instantaneous rate matrix of the restricted empirical codon model

Instantaneous rate matrix of the unrestricted empirical codon model

Parameter values for the M0 model

List of log-likelihood values for the different codon models analyzed

List of the protein families analyzed to compare SDT and the empirical codon model

Explanatory notes

These files are instead now available via this link: https://www.ebi.ac.uk/goldman-srv/ECM/SupplMat.tar.gz

Reference

[1] Kosiol, C., I. Holmes, and N. Goldman (2007) An empirical codon model for protein sequence evolution. Molecular Biology and Evolution 24:1464-1479.

Edit