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Group: FAB-lab - with tag substitution-models [42 articles]

Recent papers posted by members of the FAB-lab group with tag substitution-models
  • Accelerated molecular evolution as a consequence of transitions to mutualism
    Proceedings of the national academy of sciences, Vol. 94, No. 21. (1997), pp. 11422-11427.
    by Francois Lutzoni, Mark Pagel
    posted to substitution-models ratio-test rates methods fungi divergence comparative bacteria by rvosa to the group FAB-lab on 2008-07-11 18:54:57 as **
  • notes Estimating Evolutionary Rates in the Primate epsilon-globin Pseudogene
    (12 August 2004)
    by Toby Johnson
    posted to animals mammals primates rates software substitution-models vertebrates by rvosa to the group FAB-lab on 2008-02-08 03:13:21 as **
  • notes Molecular evolutionary dynamics of cytochrome b in Strepsirrhine primates: the phylogenetic significance of third-position transversions
    Molecular Biology and Evolution, Vol. 13 (1996), pp. 1339-1350.
    by AD Yoder, R Vilgalys, Maryellen Ruvolo
    posted to animals bibtex-import mammals mitochondrial primates sequence-evolution strepsirrhines substitution-models vertebrates by rvosa to the group FAB-lab on 2008-02-06 23:58:31 as **
  • Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cute-looking mouse lemur species
    Systematic Biology, Vol. 52, No. 5. (2003), pp. 705-716.
    by ZH Yang, AD Yoder
    posted to animals bayesian bibtex-import clock-like divergence lemuridae likelihood mammals markov-chains monte-carlo morphology primates rates substitution-models vertebrates by rvosa to the group FAB-lab on 2008-02-06 23:58:30 as **
  • notes Estimation of the Transition/Transversion Rate Bias and Species Sampling
    Journal of Molecular Evolution, Vol. 48 (1999), pp. 274-283.
    by Ziheng Yang, AD Yoder
    posted to animals bibtex-import likelihood mammals primates source-trees substitution-models vertebrates by rvosa to the group FAB-lab on 2008-02-06 23:58:30 as ** along with 1 person pradiptaray
  • notes Bayesian Phylogenetic Inference Using DNA Sequences: A Markov Chain Monte Carlo Method
    Molecular Biology and Evolution, Vol. 14, No. 7. (1997), pp. 717-724.
    by Ziheng Yang, Bruce Rannala
    posted to bayesian bibtex-import diversification extinction markov-chains monte-carlo phylogeny speciation substitution-models by rvosa to the group FAB-lab on 2008-02-06 23:58:30 as **
  • notes Likelihood Ratio Tests for Detecting Positive Selection and Application to Primate Lysozyme Evolution
    Molecular Biology and Evolution, Vol. 15, No. 5. (1998), pp. 568-573.
    by Ziheng Yang
    posted to animals bibtex-import likelihood mammals primates protein ratio-test selection substitution-models vertebrates by rvosa to the group FAB-lab on 2008-02-06 23:58:30 as **
  • PAML: a program package for phylogenetic analysis by maximum likelihood
    CABIOS, Vol. 13 (1997), pp. 555-556.
    by Ziheng Yang
    posted to bibtex-import likelihood software substitution-models by rvosa to the group FAB-lab on 2008-02-06 23:58:30 as **
  • notes Molecular Evolution of Cytochrome c Oxidase Subunit I in Primates: Is There Coevolution between Mitochondrial and Nuclear Genomes?
    Molecular Phylogenetics and Evolution, Vol. 17, No. 2. (2000), pp. 294-304.
    by Wei Wu, TR Schmidt, M Goodman, Lawrence I Grossman
    posted to animals bibtex-import dna genome mammals mitochondrial nuclear phylogenomics primates source-trees substitution-models vertebrates by rvosa to the group FAB-lab on 2008-02-06 23:58:30 as **
  • notes Molecular Evolution of Cytochrome c Oxidase Subunit IV: Evidence for Positive Selection in Simian Primates
    Journal of Molecular Evolution, Vol. 44 (1997), pp. 477-491.
    by Wei Wu, M Goodman, Margaret I Lomax, Lawrence I Grossman
    posted to animals bibtex-import dna mammals mitochondrial primates rates selection source-trees substitution-models vertebrates by rvosa to the group FAB-lab on 2008-02-06 23:58:30 as **
  • Comparison between phylogeny of introns and exons in primates
    Chinese Science Bulletin, Vol. 44, No. 21. (1999), pp. 1940-1946.
    by N Wang, R Chen
    posted to animals bibtex-import evolution inference mammals phylogeny primates sequence-evolution substitution-models vertebrates by rvosa to the group FAB-lab on 2008-02-06 23:58:29 as **
  • notes Inching toward Reality: An Improved Likelihood Model of Sequence Evolution
    Journal of Molecular Evolution, Vol. 34 (1992), pp. 3-16.
    by Jeffrey L Thorne, Hirohisa Kishino, Joseph Felsenstein
    posted to algorithms alignment bibtex-import evolution likelihood methods programming substitution-models by rvosa to the group FAB-lab on 2008-02-06 23:58:28 as **
  • notes Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
    Molecular Biology and Evolution, Vol. 10 (1993), pp. 512-526.
    by K Tamura, M Nei
    posted to animals bibtex-import hominidae mammals mitochondrial primates sequence-evolution substitution-models vertebrates by rvosa to the group FAB-lab on 2008-02-06 23:58:28 as **
  • notes Molecular Phylogeny of the New World Monkeys (Platyrrhini, Primates) Based on Two Unlinked Nuclear Genes: IRBP Intron 1 and e-Globin Sequences
    American Journal of Physical Anthropology, Vol. 100 (1996), pp. 153-179.
    by Horacio Schneider, Iracilda Sampaio, ML Harada, CML Barroso, Maria, John Czelusniak, M Goodman
    posted to animals bibtex-import cebidae evolution genetics mammals parsimony primates sequence-evolution source-trees substitution-models vertebrates by rvosa to the group FAB-lab on 2008-02-06 23:58:25 as **
  • Evolutionary rates of insertion and deletion in noncoding nucleotide sequences of Primates
    Molecular Biology and Evolution, Vol. 11, No. 3. (1994), pp. 504-512.
    by N Saitou, S Ueda
    posted to animals bibtex-import mammals primates rates sequence-evolution substitution-models vertebrates by rvosa to the group FAB-lab on 2008-02-06 23:58:24 as **
  • notes Estimating divergence dates from molecular sequences
    Molecular Biology and Evolution, Vol. 15, No. 4. (1998), pp. 442-448.
    by A Rambaut, L Bromham
    posted to animals bibtex-import birds clock-like divergence dna evolution fossils likelihood mammals methods mitochondrial phylogeny rates sequence substitution-models vertebrates by rvosa to the group FAB-lab on 2008-02-06 23:58:22 as **
  • Sampling strategies for delimiting species: Genes, individuals, and populations in the Liolaemus elongatus-kriegi complex (Squamata : Liolaemidae) in Andean-Patagonian South America
    Systematic Biology, Vol. 52, No. 2. (2003), pp. 159-185.
    by M Morando, LJ Avila, JW Sites
    posted to animals bibtex-import biodiversity biogeography data-mining evolution lizards methods phyloinformatics population population-genetics regions speciation substitution-models taxonomy vertebrates by rvosa to the group FAB-lab on 2008-02-06 23:58:18 as **
  • Performance-based selection of likelihood models for phylogeny estimation
    Systematic Biology, Vol. 52, No. 5. (2003), pp. 674-683.
    by V Minin, Z Abdo, P Joyce, J Sullivan
    posted to bayesian bibtex-import likelihood phylogeny ratio-test substitution-models by rvosa to the group FAB-lab on 2008-02-06 23:58:17 as **
  • notes Bayesian and maximum likelihood phylogenetic analyses of protein sequence data under relative branch-length differences and model violation
    BMC Evolutionary Biology, Vol. 5, No. 8. (2005)
    by Jessica C Mar, Timothy J Harlow, Mark A Ragan
    posted to bayesian bibtex-import likelihood phylogeny protein substitution-models by rvosa to the group FAB-lab on 2008-02-06 23:58:16 as **
  • Out of Africa: molecular phylogenetics and biogeography of Wolffiella (Lemnaceae)
    Biological Journal of the Linnean Society, Vol. 79, No. 4. (2003), pp. 565-576.
    by RT Kimball, DJ Crawford, DH Les, E Landolt
    posted to bibtex-import biogeography classification data-mining morphology plants substitution-models taxonomy by rvosa to the group FAB-lab on 2008-02-06 23:58:15 as **
  • Molecular systematics and adaptive radiation of Hawaii's endemic damselfly genus Megalagrion (Odonata : Coenagrionidae)
    Systematic Biology, Vol. 52, No. 1. (2003), pp. 89-109.
    by S Jordan, C Simon, D Polhemus
    posted to adaptation animals bayesian bibtex-import insects invertebrates likelihood mitochondrial nuclear phylogeny radiation ratio-test speciation substitution-models topology by rvosa to the group FAB-lab on 2008-02-06 23:58:14 as **
  • When do parasites fail to speciate in response to host speciation?
    Systematic Biology, Vol. 52, No. 1. (2003), pp. 37-47.
    by KP Johnson, RJ Adams, RDM Page, DH Clayton
    posted to animals bibtex-import birds dna insects invertebrates mitochondrial nuclear parasitism phylogeny population-genetics rates speciation substitution-models topology vertebrates by rvosa to the group FAB-lab on 2008-02-06 23:58:14 as **
  • Outgroup misplacement and phylogenetic inaccuracy under a molecular clock - A simulation study
    Systematic Biology, Vol. 52, No. 2. (2003), pp. 229-238.
    by BR Holland, D Penny, MD Hendy
    posted to bibtex-import clock-like likelihood parsimony phenetics simulation substitution-models by rvosa to the group FAB-lab on 2008-02-06 23:58:12 as **
  • notes Success of Maximum Likelihood Phylogeny Inference in the Four-Taxon Case
    Molecular Biology and Evolution, Vol. 12, No. 1. (1995), pp. 152-162.
    by Brandon S Gaut, Paul O Lewis
    posted to bibtex-import likelihood phylogeny ratio-test substitution-models by rvosa to the group FAB-lab on 2008-02-06 23:58:08 as **
  • notes Inferring Pattern and Process: Maximum-Likelihood Implementation of a Nonhomogeneous Model of DNA Sequence Evolution for Phylogenetic Analysis
    Molecular Biology and Evolution, Vol. 15, No. 7. (1998), pp. 871-879.
    by Nicolas Galtier, Manolo Gouy
    posted to bibtex-import genetics likelihood phylogeny sequence-evolution substitution-models by rvosa to the group FAB-lab on 2008-02-06 23:58:08 as **
  • Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics
    Systematic Biology, Vol. 52, No. 5. (2003), pp. 665-673.
    by P Erixon, B Svennblad, T Britton, B Oxelman
    posted to bayesian bibtex-import likelihood markov-chains methods monte-carlo simulation substitution-models by rvosa to the group FAB-lab on 2008-02-06 23:58:07 as **
  • Insulin-like growth factor II intron sequences support the hominoid rate-slowdown hypothesis
    Molecular Phylogenetics and Evolution, Vol. 2, No. 315-321. (1993)
    by DL Ellsworth, Hewett D Emmett, WH Li
    posted to animals bibtex-import dna genetics hominidae humans mammals nuclear primates rates substitution-models vertebrates by rvosa to the group FAB-lab on 2008-02-06 23:58:07 as **
  • notes Molecular Evidence from the Nuclear Genome for the Time Frame of Human Evolution
    Journal of Molecular Evolution, Vol. 44(Suppl 1) (1997), pp. S121-S132.
    by S Easteal, G Herbert
    posted to animals bibtex-import clock-like evolution hominidae humans mammals primates rates sequence substitution-models vertebrates by rvosa to the group FAB-lab on 2008-02-06 23:58:07 as **
  • notes Hominoid phylogeny estimated by model selection using goodness of fit significance tests
    Molecular Phylogenetics and Evolution, Vol. 4 (1995), pp. 283-290.
    by John Czelusniak, M Goodman
    posted to animals bibtex-import mammals models primates source-trees substitution-models vertebrates by rvosa to the group FAB-lab on 2008-02-06 23:58:06 as **
  • Rates of transition and transversion in coding sequences since the human-rodent divergence
    Genomics, Vol. 20 (1994), pp. 386-396.
    by DW Collins, TH Jukes
    posted to animals bibtex-import mammals primates rates rodents substitution-models vertebrates by rvosa to the group FAB-lab on 2008-02-06 23:58:05 as **
  • notes Accelerated Evolution of Cytochrome b in Simian Primates: Adaptive Evolution in Concert with Other Mitochondrial Proteins?
    Journal of Molecular Evolution, Vol. 47 (1998), pp. 249-257.
    by TD Andrews, LS Jermiin, S Easteal
    posted to adaptation animals bibtex-import dna genetics mammals mitochondrial primates rates source-trees substitution-models vertebrates by rvosa to the group FAB-lab on 2008-02-06 23:58:02 as **
  • notes Evolution of the Primate Cytochrome c Oxidase Subunit II Gene
    Journal of Molecular Evolution, Vol. 38 (1994), pp. 215-231.
    by RM Adkins, RL Honeycutt
    posted to animals bibtex-import dna evolution mammals mitochondrial primates rates source-trees substitution-models vertebrates by rvosa to the group FAB-lab on 2008-02-06 23:58:01 as **
  • notes Improved Dating of the Human Chimpanzee Separation in the Mitochondrial-DNA Tree - Heterogeneity among Amino-Acid Sites
    Journal of Molecular Evolution, Vol. 40, No. 6. (1995), pp. 622-628.
    by J Adachi, M Hasegawa
    posted to amino-acid animals bibtex-import clock-like dna hominidae humans likelihood mammals mitochondrial phylogeny primates sequence source-trees substitution-models vertebrates by rvosa to the group FAB-lab on 2008-02-06 23:58:01 as **
  • The Problem of Rooting Rapid Radiations
    Mol Biol Evol, Vol. 24, No. 11. (1 November 2007), pp. 2400-2411.
    by Liat Shavit, David Penny, Michael D Hendy, Barbara R Holland
    posted to adaptation diversification likelihood parsimony phylogeny radiation substitution-models by rvosa to the group FAB-lab on 2007-11-28 02:49:08 as **
  • Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selection.
    Philos Trans R Soc Lond B Biol Sci, Vol. 359, No. 1450. (29 October 2004), pp. 1477-1483.
    by TJ Near, MJ Sanderson
    posted to clock-like divergence fossils inference likelihood reconstruction substitution-models by rvosa to the group FAB-lab on 2005-10-13 12:58:12 as **
  • Maximum-Likelihood Estimation of Population Divergence Times and Population Phylogeny in Models without Mutation
    Evolution, Vol. 52, No. 3. (1998), pp. 669-677.
    by Rasmus Nielsen, Joanna L Mountain, John P Huelsenbeck, Montgomery Slatkin
    posted to bayesian clock-like divergence likelihood reconstruction substitution-models by rvosa to the group FAB-lab on 2005-10-12 21:39:39 as ** along with 1 person jmeppley
  • Temporal scaling of molecular evolution in primates and other mammals.
    Mol Biol Evol, Vol. 3, No. 3. (May 1986), pp. 205-221.
    by PD Gingerich
    posted to clock-like comparative divergence phylogeny reconstruction substitution-models by rvosa to the group FAB-lab on 2005-10-12 21:28:42 as **
  • Recombination and the molecular clock.
    Mol Biol Evol, Vol. 17, No. 10. (October 2000), pp. 1578-1579.
    by MH Schierup, J Hein
    posted to clock-like likelihood phylogeny ratio-test substitution-models by rvosa to the group FAB-lab on 2005-10-12 21:20:48 as **
  • Unveiling the molecular clock in the presence of recombination.
    Mol Biol Evol, Vol. 18, No. 10. (October 2001), pp. 1976-1978.
    by D Posada
    posted to clock-like likelihood phylogeny ratio-test substitution-models by rvosa to the group FAB-lab on 2005-10-12 21:18:32 as **
  • Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo.
    Mol Biol Evol, Vol. 21, No. 6. (June 2004), pp. 1123-1133.
    by JP Huelsenbeck, B Larget, ME Alfaro
    posted to bayesian clock-like likelihood phylogeny ratio-test substitution-models by rvosa to the group FAB-lab on 2005-10-12 21:11:30 as ** along with 1 person aprasad
  • Using models of nucleotide evolution to build phylogenetic trees.
    Dev Comp Immunol, Vol. 29, No. 3. (2005), pp. 211-227.
    by DH Bos, D Posada
    posted to clock-like likelihood phylogeny ratio-test substitution-models by rvosa to the group FAB-lab on 2005-10-12 21:10:26 as **
  • Maximum-Likelihood Models for Combined Analyses of Multiple Sequence Data
    J Mol Evol, Vol. 42, No. 5. (May 1996), pp. 587-596.
    by Z Yang
    posted to clock-like likelihood phylogeny ratio-test substitution-models by rvosa to the group FAB-lab on 2005-10-12 20:41:58 as **
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