diff --git src/hg/makeDb/trackDb/mouse/mm9/multiz30way.html src/hg/makeDb/trackDb/mouse/mm9/multiz30way.html
index b40b57165a9..846e625e69c 100644
--- src/hg/makeDb/trackDb/mouse/mm9/multiz30way.html
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@@ -354,30 +354,61 @@
scores reflect the phylogeny (including branch lengths) of the species in
question, a continuous-time Markov model of the nucleotide substitution
process, and a tendency for conservation levels to be autocorrelated along
the genome (i.e., to be similar at adjacent sites). The general reversible
(REV) substitution model was used. Unlike many conservation-scoring programs,
note that phastCons does not rely on a sliding window
of fixed size; therefore, short highly-conserved regions and long moderately
conserved regions can both obtain high scores. More information about
phastCons can be found in Siepel et al. 2005.
PhastCons currently treats alignment gaps as missing data, which
sometimes has the effect of producing undesirably high conservation scores
in gappy regions of the alignment. We are looking at several possible ways
of improving the handling of alignment gaps.
+Data Access
+
+The alignments and the conservation scores can be retrieved for a single region or for a list of
+regions with the Table Browser,
+which returns the alignments in MAF format and the scores as wiggle data. The scores and the
+conserved elements, though not the alignments, can also be joined with other annotations in the
+Data Integrator. For automated access, our REST API serves the alignment and conservation tracks
+individually, by name.
+
+
+The files behind this track can be downloaded from our download server:
+
+
+
+Genome-wide alignment files are large. Among our command-line programs, mafsInRegion,
+mafSpeciesSubset and mafFrags pull out a region, a subset of species, or the
+alignment underlying a gene. They can be downloaded from the utilities directory, and
+each one prints its usage when run with no arguments. See our Data Access FAQ for more information.
+
+
Credits
This track was created using the following programs:
- Alignment tools: blastz and multiz by Minmei Hou, Scott Schwartz and Webb
Miller of the Penn State Bioinformatics Group
- Chaining and Netting: axtChain, chainNet by Jim Kent at UCSC
- Conservation scoring: PhastCons, phyloFit, tree_doctor, msa_view by
Adam Siepel while at UCSC, now at Cold Spring Harbor Laboratory
- MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows
by Richard Burhans, Penn State; genePredToMafFrames by Mark Diekhans, UCSC
- Tree image generator: phyloPng by Galt Barber, UCSC
- Conservation track display: Kate Rosenbloom, Hiram Clawson (wiggle
display), and Brian Raney (gap annotation and codon framing) at UCSC