Commits for hiram

v258_preview to v258_preview2 (2011-09-27 to 2011-10-04) v258

• add search rules for gold and ctgPos2
  • src/hg/makeDb/trackDb/cow/bosTau6/trackDb.ra - lines changed 16, context: html, text, full: html, text
• rerun xenTro3 lastz with parameters that produce a bit more coverage
  • src/hg/makeDb/doc/melGal1.txt - lines changed 60, context: html, text, full: html, text
• initial diagram for xenTro3 9-way alignment
  • src/hg/htdocs/images/phylo/xenTro3_9way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• repeat the melGal1 alignment and start the 9-way
  • src/hg/makeDb/doc/xenTro3.txt - lines changed 243, context: html, text, full: html, text
• have 9-way multiz with gene and gap annotations
  • src/hg/makeDb/doc/xenTro3.txt - lines changed 206, context: html, text, full: html, text
• done with 4D site tree estimate
  • src/hg/makeDb/doc/xenTro3.txt - lines changed 122, context: html, text, full: html, text
• phastCons done for 9-way
  • src/hg/makeDb/doc/xenTro3.txt - lines changed 248, context: html, text, full: html, text
• note about phyloBoot never finishing
  • src/hg/makeDb/doc/sacCer3.txt - lines changed 2, context: html, text, full: html, text
• phyloP done for 9-way and working on downloads
  • src/hg/makeDb/doc/xenTro3.txt - lines changed 256, context: html, text, full: html, text
• done with 9-way alignment
  • src/hg/makeDb/doc/xenTro3.txt - lines changed 4, context: html, text, full: html, text
• initial contents copied from anoCar2 and updated for xenTro3
  • src/hg/makeDb/trackDb/xenTro/xenTro3/cons9way.html - lines changed 400, context: html, text, full: html, text
• adding cons9way
  • src/hg/makeDb/trackDb/xenTro/xenTro3/trackDb.ra - lines changed 104, context: html, text, full: html, text