File Changes for hiram

v252_base to v253_preview (2011-06-07 to 2011-06-14) v253

• src/hg/htdocs/images/phylo/ce10.9way.png
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    ce10 9way multiz tree
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    incorrect file name
• src/hg/htdocs/images/phylo/ce10_9way.png
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    correct file name
• src/hg/makeDb/doc/caeAng1.txt
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    finished with all lastz operations to ce10
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    makeDownloads.pl has been run and all README files in download directories have been edited
• src/hg/makeDb/doc/caeJap4.txt
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    lastz runs done for almost all to ce10
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    makeDownloads.pl has been run and all README files in download directories have been edited
• src/hg/makeDb/doc/caePb3.txt
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    finished with all lastz operations to ce10
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    makeDownloads.pl has been run and all README files in download directories have been edited
• src/hg/makeDb/doc/caeRem4.txt
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    lastz runs done for almost all to ce10
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    makeDownloads.pl has been run and all README files in download directories have been edited
• src/hg/makeDb/doc/caeSp111.txt
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    lastz runs done for almost all to ce10
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    makeDownloads.pl has been run and all README files in download directories have been edited
• src/hg/makeDb/doc/caeSp71.txt
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    lastz runs done for almost all to ce10
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    makeDownloads.pl has been run and all README files in download directories have been edited
• src/hg/makeDb/doc/caeSp91.txt
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    lastz runs done for almost all to ce10
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    makeDownloads.pl has been run and all README files in download directories have been edited
• src/hg/makeDb/doc/cb4.txt
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    lastz runs done for almost all to ce10
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    makeDownloads.pl has been run and all README files in download directories have been edited
• src/hg/makeDb/doc/ce10.txt
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    lastz runs done for almost all to ce10
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    finished with all lastz operations to ce10
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    9-way multiz initial done and ensGene v62 loaded
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    maf gaps annotated and phastCons and phyloP runs done
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    downloads have been constructed
• src/hg/makeDb/genbank/etc/align.dbs
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    adding caeJap4 to the build
• src/hg/makeDb/genbank/etc/hgwdev.dbs
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    adding caeJap4 to the build
• src/hg/makeDb/trackDb/makefile
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    adding caePb3 to the build
• src/hg/makeDb/trackDb/worm/ce10/cons9way.html
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    text from ce9 cons10way and edited for this 9-way alignment
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    reference to hgdownload-test instead of hgdownload
• src/hg/makeDb/trackDb/worm/ce10/trackDb.ra
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    adding 9-way multiple alignment definition
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    perhaps better order of organisms in phylo distance maybe
• src/hg/utils/phyloTrees/nematode.14way.nh
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    nematode tree enlarged
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    adjust some branch lengths given lastz chain net coverage