We have computed estimates of the average dn/ds (a.k.a. omega) over all sites of each transcript (tx) using two methods ("SLR" and "M0"). (SLR and M0 methods described below.)

These results are presented in four files:

SLR results sorted by region/tx:
http://www.ebi.ac.uk/goldman-srv/encode/encode_SEP2005/All_regions/tx_dnds_SLR.prank.enctree
(file contains: region/gene_name-tx_id/omega/no_codons_in_tx)

SLR results sorted by estimated value of omega:
http://www.ebi.ac.uk/goldman-srv/encode/encode_SEP2005/All_regions/tx_dnds_SLR.sorted.prank.enctree
(file contains: region/gene_name-tx_id/omega/no_codons_in_tx)

M0 results sorted by region/tx:
http://www.ebi.ac.uk/goldman-srv/encode/encode_SEP2005/All_regions/tx_dnds_M0.prank.enctree
(file contains: region/gene_name-tx_id/omega)

SLR results sorted by estimated value of omega:
http://www.ebi.ac.uk/goldman-srv/encode/encode_SEP2005/All_regions/tx_dnds_M0.sorted.prank.enctree
(file contains: region/gene_name-tx_id/omega)

SLR is a method that estimates the selective pressure via an omega estimate at each site of a tx. For a tx-wide measure, we take the mean of the sitewise inferences within the tx. M0 is a model that assumes the same omega at every site, and estimates this omega. Further details on request.