title: Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.
abstract: BACKGROUND
  As genomes evolve after speciation, gene content, coding sequence, gene expression, and splicing all diverge with time from ancestors with close relatives. A minimum evolution general method for continuous character analysis in a phylogenetic perspective is presented that allows for reconstruction of ancestral character states and for measuring along branch evolution.
  
  
  RESULTS
  A software package for reconstruction of continuous character traits, like relative gene expression levels or alternative splice site usage data is presented and is available for download at http://www.rossnes.org/phyrex. This program was applied to a primate gene expression dataset to detect transcription factor binding sites that have undergone substitution, potentially having driven lineage-specific differences in gene expression.
  
  
  CONCLUSIONS
  Systematic analysis of lineage-specific evolution is becoming the cornerstone of comparative genomics. New methods, like phyrex, extend the capabilities of comparative genomics by tracing the evolution of additional biomolecular processes.
authors.affiliation: Bergen Centre for Computational Science, University of Bergen, 5020 Bergen, Norway. roald@rossnes.org
authors.forename: Roald
authors.initials: R
authors.lastname: Rossnes
authors.forename: Ingvar
authors.initials: I
authors.lastname: Eidhammer
authors.forename: David A
authors.initials: DA
authors.lastname: Liberles
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D005075:Biological Evolution; D001921:Brain / Q000378:metabolism; D019070:Cell Lineage; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D015870:Gene Expression; D005786:Gene Expression Regulation; D016678:Genome; D023281:Genomics; D006801:Humans; D008099:Liver / Q000378:metabolism; D008957:Models, Genetic; D008969:Molecular Sequence Data; D002679:Pan troglodytes / Q000235:genetics; D010802:Phylogeny; D011148:Pongo pygmaeus / Q000235:genetics; D012333:RNA, Messenger / Q000378:metabolism*; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D012333:RNA, Messenger