Hi,
According to the README file
phylogenetic trees
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz44way/44way.nh
and
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz44way/commonNames.nh
should differ only by names:
"Files in this directory:
- 44way.nh - phylogenetic tree for the phastCons and phyloP calculations
- commonNames.nh - same as 44way.nh with the UCSC database name
replace by the common name for the species"
However, it is not the case - branch lengths are also different. Just look at
the first lines for a example:
44way.nh:
(((((((((((((((((hg18:0.003731,panTro2:0.005501):0.013010,gorGor1:0.01):0.01,
commonNames.nh:
(((((((((((((((((Human:0.006591,Chimp:0.006639):0.002184,Gorilla:0.009411):0.009942,
Sincerely,
Gregory
--
Gregory Kryukov
Harvard Medical School
Brigham & Women's Hospital
Division of Genetics
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Boston, MA 02115
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