Commits for hiram

v260_base to v261_preview (2011-12-06 to 2011-12-13) v261

• initial contents seem to work
  • src/hg/utils/phyloTrees/speciesList.sh - lines changed 21, context: html, text, full: html, text
• rearrange the fish a bit, and coelacanth, alligator, crocodile
  • src/hg/utils/phyloTrees/57way.nh - lines changed 9, context: html, text, full: html, text
• now with new distances for the primates from the 11-way gorGor3 calculations
  • src/hg/utils/phyloTrees/57way.nh - lines changed 5, context: html, text, full: html, text
• annotation done, phastCons and phyloP done for 11-way multiz
  • src/hg/makeDb/doc/gorGor3.txt - lines changed 816, context: html, text, full: html, text
• initial text derived from xenTro3
  • src/hg/makeDb/trackDb/gorilla/gorGor3/cons11way.html - lines changed 406, context: html, text, full: html, text
• adding cons11way track
  • src/hg/makeDb/trackDb/gorilla/gorGor3/trackDb.ra - lines changed 104, context: html, text, full: html, text
• allow Encode html hierarchy to be pulled
  • src/product/scripts/updateHtml.sh - lines changed 8, context: html, text, full: html, text
• download data for 11-way business is done
  • src/hg/makeDb/doc/gorGor3.txt - lines changed 80, context: html, text, full: html, text
• hgPal downloads constructed for 11-way
  • src/hg/makeDb/doc/gorGor3.txt - lines changed 60, context: html, text, full: html, text
• set the upstreamGeneTbl and upstreamMaf for gorGor3
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 2, context: html, text, full: html, text