Hi Gregory, One of our developers looked in to this and found that the 44way.nh file contained incorrect branch lengths. This file has been updated and now contains the correct branch lengths, which match the branch lengths in the commonNames.nh file.
Thank you for bringing this to our attention. Katrina Learned UCSC Genome Bioinformatics Group Grigoriy Kryukov wrote: > 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 > > > > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
