Supplementary data for "Phylogenetic estimation of context-dependent substitution rates by maximum likelihood," Mol. Biol. Evol. 21:468-488, 2004.

• multiple alignment of 9 mammalian sequences in the CFTR region [T1.msa.gz]
  (sequence data were generated by the NIH Comparative Sequencing Program, have been described by Thomas et al., Nature, 424:788-793, and are available at http://www.nisc.nih.gov/data; the alignment was produced by the TBA program)

• sub-alignments of ancestral repeats (ARs), original and cleaned [T1-AR.msa.gz][T1-AR.clean.msa.gz]
  The coordinates of the ARs in the human sequence are also available [T1-AR.gff]

• source alignments of RefSeq genes and orthologous mRNAs, orig. and cleaned [mrna-src.tgz]
  (alignments were produced by the T-COFFEE program, using the "cdna_fast_pair" option)

• complete mRNA alignment (concatenated cleaned alignments) [all-mrna.msa.gz]

• parameter estimates for AR alignment [ar-mods.tgz]

• parameter estimates for mRNA alignment [mrna-mods.tgz]