Phylogenomics pp 133-144 | Cite as

Phylogenomic Resources at the UCSC Genome Browser

  • Kate Rosenbloom
  • James Taylor
  • Stephen Schaeffer
  • Jim Kent
  • David Haussler
  • Webb Miller
Part of the Methods in Molecular Biology™ book series (MIMB, volume 422)


The UC Santa Cruz Genome Browser provides a number of resources that can be used for phylogenomic studies, including (1) whole-genome sequence data from a number of vertebrate species, (2) pairwise alignments of the human genome sequence to a number of other vertebrate genome, (3) a simultaneous alignment of 17 vertebrate genomes (most of them incompletely sequenced) that covers all of the human sequence, (4) several independent sets of multiple alignments covering 1% of the human genome (ENCODE regions), (5) extensive sequence annotation for interpreting those sequences and alignments, and (6) sequence, alignments, and annotations from certain other species, including an alignment of nine insect genomes. We illustrate the use of these resources in the context of assigning rare genomic changes to the branch of the phylogenetic tree where they appear to have occurred, or of looking for evidence supporting a particular possible tree topology. Sample source code for performing such studies is available.

Key Words

Evolutionary event phylogenetic tree interspersed repeat chromosomal break 


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Copyright information

© Humana Press Inc., Totowa, NJ 2008

Authors and Affiliations

  • Kate Rosenbloom
    • 1
  • James Taylor
    • 2
  • Stephen Schaeffer
    • 3
  • Jim Kent
    • 1
  • David Haussler
    • 4
  • Webb Miller
    • 2
  1. 1.Center for Biomolecular Science and EngineeringUniversity of CaliforniaSanta Cruz
  2. 2.Center for Comparative Genomics and BioinformaticsPenn StateUniversity Park
  3. 3.Department of BiologyPenn StateUniversity Park
  4. 4.Howard Hughes Medical InstituteUniversity of CaliforniaSanta Cruz

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