NOTUNG: A program for dating gene duplications and optimizing gene family trees

Journal of Computational Biology

Volumn 7, Issue 3-4, 2000, Pages 429-447

  Chen, K ^a   Durand, D ^b   Farach Colton, M ^c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b CARNEGIE MELLON UNIVERSITY   (United States)

^c RUTGERS UNIVERSITY   (United States)

Author keywords

Duplication loss models; Evolutionary tree; Gene duplication; Gene family; Phylogeny

Indexed keywords

AUTOMATION; COMPUTER PROGRAM; CONFERENCE PAPER; GENE DUPLICATION; GENE SEQUENCE; MAIZE; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; VERTEBRATE; YEAST;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; EVOLUTION; GENE DUPLICATION; HUMANS; MODELS, GENETIC; MULTIGENE FAMILY; PHYLOGENY; SOFTWARE; TIME FACTORS;

VERTEBRATA; ZEA MAYS;

EID: 0033692378     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/106652700750050871     Document Type: Conference Paper

References (33)

1. Least common ancestors revisited
2. Notung: Dating gene duplications using gene family trees
3. A leisurely look at the bootstrap, jackknife, and cross-validation
4. Evolutionary significance of intra-genome duplications on human chromosomes
5. Comparison of annotating duplication, tree mapping, and copying as methods to compare gene trees with species trees
6. Duplication-based measures of difference between gene and species trees
7. Life with 6000 genes
8. Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences
9. Phylogenetic position of the order lagomorpha (rabbits, hares and allies)
10. Reconstruction of ancient phylogenies
11. New algorithms for the duplication-loss model
12. Phylogenetic tests of the hypothesis of block duplication of homologous genes on human chromosomes 6, 9, and 1
13. Phylogenies of developmentally important proteins do not support the hypothesis of two rounds of genome duplication early in vertebrate history
14. New insights into the genomic organization and origin of the major histocompatibility complex: Role of chromosomal (genome) duplication in the emergence of the adaptive immune system
15. From gene trees to species trees
16. From gene trees to species trees
17. A new version of the rdp (Ribosomal Database Project)
18. Increasing genomic complexity by gene duplication and the origin of vertebrates
19. A biologically consistent model for comparing molecular phylogenies
20. Maps between trees and cladistic analysis of historical associations among genes, organisms and areas
21. Reconciled trees and incongruent gene and species trees
22. From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem
23. Ancient large-scale genome duplications: Phylogenetic and linkage analyses shed light on chordate genome evolution
24. Newly indentified paralogous groups on mouse chromosomes 5 and 11 reveal the age of a t-box cluster duplication
25. Eukaryote genome duplication - Where's the evidence?
26. Gene trees and species trees: The gene-duplication problem is fixed-parameter tractable
27. Phylogeny inference
28. Molecular evidence for an ancient duplication of the entire yeast genome
29. On a Mirkin-Muchnik-Smith conjecture for comparing molecular phylogenies