GIGA: a simple, efficient algorithm for gene tree inference in the genomic age
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[1] W. Maddison,et al. Inferring phylogeny despite incomplete lineage sorting. , 2006, Systematic biology.
[2] Jonathan P. Bollback,et al. Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology , 2001, Science.
[3] G. Olsen,et al. Ribosomal RNA: a key to phylogeny , 1993, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
[4] T. Jukes. CHAPTER 24 – Evolution of Protein Molecules , 1969 .
[5] B. Birren,et al. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae , 2004, Nature.
[6] B. Rannala,et al. Phylogenetic inference using whole genomes. , 2008, Annual review of genomics and human genetics.
[7] S. Jeffery. Evolution of Protein Molecules , 1979 .
[8] Christophe Dessimoz,et al. Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods , 2009, PLoS Comput. Biol..
[9] D. Eisenberg,et al. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[10] T. Tuller,et al. Inferring phylogenetic networks by the maximum parsimony criterion: a case study. , 2006, Molecular biology and evolution.
[11] C Sander,et al. Predicting protein structure using hidden Markov models , 1997, Proteins.
[12] G. Moore,et al. Descent of mammalian alpha globin chain sequences investigated by the maximum parsimony method. , 1972, Journal of molecular biology.
[13] K. Holsinger. The neutral theory of molecular evolution , 2004 .
[14] Lincoln Stein,et al. nGASP – the nematode genome annotation assessment project , 2008, BMC Bioinformatics.
[15] D. Robinson,et al. Comparison of phylogenetic trees , 1981 .
[16] Alan M. Moses,et al. Widespread Discordance of Gene Trees with Species Tree in Drosophila: Evidence for Incomplete Lineage Sorting , 2006, PLoS genetics.
[17] Joaquín Dopazo,et al. PhylomeDB: a database for genome-wide collections of gene phylogenies , 2007, Nucleic Acids Res..
[18] M. P. Cummings. PHYLIP (Phylogeny Inference Package) , 2004 .
[19] Leon Goldovsky,et al. The net of life: reconstructing the microbial phylogenetic network. , 2005, Genome research.
[20] Toni Gabaldón,et al. The Tree versus the Forest: The Fungal Tree of Life and the Topological Diversity within the Yeast Phylome , 2009, PloS one.
[21] Avi Pfeffer,et al. Automatic genome-wide reconstruction of phylogenetic gene trees , 2007, ISMB/ECCB.
[22] Ziheng Yang. PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.
[23] Matthew J. Betts,et al. Optimal Gene Trees from Sequences and Species Trees Using a Soft Interpretation of Parsimony , 2006, Journal of Molecular Evolution.
[24] Nicholas Hamilton,et al. Phylogenetic identification of lateral genetic transfer events , 2006, BMC Evolutionary Biology.
[25] Matthew D. Rasmussen,et al. Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes. , 2007, Genome research.
[26] Tero Aittokallio,et al. Model-based prediction of sequence alignment quality , 2008, Bioinform..
[27] Albert J. Vilella,et al. EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. , 2009, Genome research.
[28] Darren A. Natale,et al. The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.
[29] Dannie Durand,et al. A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction , 2005, RECOMB.
[30] Morris Goodman,et al. Phylogenetic origins and adaptive evolution of avian and mammalian haemoglobin genes , 1982, Nature.
[31] Li Ni,et al. The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species , 2009, PLoS Comput. Biol..
[32] Tao Liu,et al. TreeFam: 2008 Update , 2007, Nucleic Acids Res..
[33] Dannie Durand,et al. NOTUNG: A Program for Dating Gene Duplications and Optimizing Gene Family Trees , 2000, J. Comput. Biol..
[34] William R. Taylor,et al. The rapid generation of mutation data matrices from protein sequences , 1992, Comput. Appl. Biosci..
[35] E. Birney,et al. EGASP: the human ENCODE Genome Annotation Assessment Project , 2006, Genome Biology.
[36] O. Gascuel,et al. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.
[37] Allan C. Wilson,et al. Construction of phylogenetic trees for proteins and nucleic acids: Empirical evaluation of alternative matrix methods , 1978, Journal of Molecular Evolution.
[38] T. Jukes,et al. The neutral theory of molecular evolution. , 2000, Genetics.
[39] Alexander C. J. Roth,et al. Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits , 2006, Nucleic acids research.
[40] Yuying Tian,et al. GeneTrees: a phylogenomics resource for prokaryotes , 2006, Nucleic Acids Res..
[41] H. Munro,et al. Mammalian protein metabolism , 1964 .
[42] Anushya Muruganujan,et al. PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium , 2009, Nucleic Acids Res..
[43] M. Lynch,et al. The altered evolutionary trajectories of gene duplicates. , 2004, Trends in genetics : TIG.
[44] N. Saitou,et al. The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.