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Tag paml [22 articles]

Recent papers classified by the tag paml.
  • PAML: a program package for phylogenetic analysis by maximum likelihood.
    Comput Appl Biosci, Vol. 13, No. 5. (October 1997), pp. 555-556.
    by Z Yang
    posted to coccipaper codon_model methods molecular_evolution paml phylogenetics by stajich on 2008-04-19 21:34:23 as ** along with 13 people and 3 groups alexeid druvus jmjimenez bjorns chrn chad_davis indigoviolet penka BioNica pv usagi-kirin tharris skumagai EisenLab Nie Berkeley Mycology
  • Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages.
    Mol Biol Evol, Vol. 19, No. 6. (June 2002), pp. 908-917.
    by Z Yang, R Nielsen
    posted to coccipaper codon_model molecular_evolution paml selection selection_test by stajich on 2008-04-19 21:31:03 as ** along with 4 people and 2 groups skembel stevanspringer operon Garamonfok FAB-lab Berkeley Mycology
  • PAML 4: Phylogenetic Analysis by Maximum Likelihood
    Mol Biol Evol (4 May 2007), msm088.
    by Ziheng Yang
    posted to coccipaper codon_model molecular_evolution paml selection selection_test by stajich on 2008-04-19 21:29:02 as ** along with 9 people and 1 group druvus operon akifumi hdopazo BioNica ryanraaum RamuAnandakrishnan CharlesM Ema Berkeley Mycology
  • Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection
    Molecular Biology and Evolution, Vol. 22, No. 4. (April 2005), pp. 1107-1118.
    by Ziheng Yang, Wendy S Wong, Rasmus Nielsen
    posted to coccipaper codon_model molecular_evolution paml positive_selecion selection selection_test by stajich on 2008-04-19 21:29:42 as ** along with 6 people and 1 group rabu BioNica Natasha Garamonfok skumagai CharlesM Berkeley Mycology
  • Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage.
    Mol Biol Evol (3 January 2008)
    by Ziheng Yang, Rasmus Nielsen
    posted to codon_model molecular_evolution paml selection selection_test by stajich on 2008-04-19 21:28:47 as ** along with 4 people and 1 group operon BioNica cjeans gjuggler Berkeley Mycology
  • A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution.
    J Mol Evol, Vol. 59, No. 1. (July 2004), pp. 121-132.
    by JP Bielawski, Z Yang
    posted to codon family gene likelihood maximum molevoltestis paml positive selection by skumagai on 2008-06-06 01:42:34 as read along with 1 person and 1 group stevanspringer FAB-lab
  • Maximum-Likelihood Analysis of Molecular Adaptation in Abalone Sperm Lysin Reveals Variable Selective Pressures Among Lineages and Sites
    Mol Biol Evol, Vol. 17, No. 10. (1 October 2000), pp. 1446-1455.
    by Ziheng Yang, Willie J Swanson, Victor D Vacquier
    posted to abalone codon likelihood maximum molevoltestis paml positive selection sperm substitution by skumagai on 2008-06-06 16:21:33 as read along with 1 person and 1 group stevanspringer FAB-lab
  • Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution.
    Mol Biol Evol, Vol. 15, No. 5. (May 1998), pp. 568-573.
    by Z Yang
    posted to evolution paml positiveselection by Garamonfok on 2008-03-05 17:46:09 as read along with 3 people gjuggler AaronDarling usagi-kirin
  • Human PAML browser: a database of positive selection on human genes using phylogenetic methods.
    Nucleic Acids Res, Vol. 36, No. Database issue. (January 2008)
    by GC Nickel, D Tefft, MD Adams
    posted to evolution paml positiveselection tools by Garamonfok on 2008-02-09 15:43:26 as ***** along with 1 person operon
  • Recombination in AIDS viruses.
    J Mol Evol, Vol. 40, No. 3. (March 1995), pp. 249-259.
    by DL Robertson, BH Hahn, PM Sharp
    posted to adaptiveevolution evolution paml positiveselection by Garamonfok on 2008-03-05 17:42:25 as read
  • Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites
    Genetics, Vol. 155, No. 1. (1 May 2000), pp. 431-449.
    by Ziheng Yang, Rasmus Nielsen, Nick Goldman, Anne-Mette K Pedersen
    posted to evolution paml positiveselection by Garamonfok on 2008-03-05 17:43:51 as read along with 8 people druvus fernan BioNica Natasha dylan77 tale gjuggler emptyhb
  • Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level
    Mol Biol Evol, Vol. 22, No. 12. (1 December 2005), pp. 2472-2479.
    by Jianzhi Zhang, Rasmus Nielsen, Ziheng Yang
    posted to evolution paml positiveselection by Garamonfok on 2008-03-05 17:51:05 as ** along with 5 people and 1 group stevanspringer AaronDarling usagi-kirin mingzhi CharlesM FAB-lab
  • Evidence for positive selection on the E2 gene of bovine viral diarrhoea virus type 1
    Virus Genes, Vol. 35, No. 3. (24 December 2007), pp. 629-634.
    by Fangqiang Tang, Chuyu Zhang
    posted to evolution paml positiveselection by Garamonfok on 2008-03-11 10:17:25 as **
  • Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models.
    Mol Biol Evol, Vol. 17, No. 1. (January 2000), pp. 32-43.
    by Z Yang, R Nielsen
    posted to evolution paml positiveselection by Garamonfok on 2008-03-05 17:57:19 as ** along with 8 people and 1 group bjorns fernan hdopazo BioNica timflutre ankur_iitg RamuAnandakrishnan Ema BioinfoCIPF
  • Frequent False Detection of Positive Selection by the Likelihood Method with Branch-Site Models
    Mol Biol Evol, Vol. 21, No. 7. (1 July 2004), pp. 1332-1339.
    by Jianzhi Zhang
    posted to evolution paml positiveselection by Garamonfok on 2008-03-05 17:53:04 as ** along with 1 person and 1 group rvosa FAB-lab
  • A Space-Time Process Model for the Evolution of DNA Sequences
    Genetics, Vol. 139, No. 2. (1 February 1995), pp. 993-1005.
    by Z Yang
    posted to gamma model paml phylogenetics by bpb on 2007-12-13 15:48:31 as ** along with 3 people pradiptaray tale friendpine
  • Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene
    Genetics, Vol. 148, No. 3. (1 March 1998), pp. 929-936.
    by Rasmus Nielsen, Ziheng Yang
    posted to paml by BioNica on 2006-09-29 12:33:26 as read
  • Detecting amino acid sites under positive selection and purifying selection.
    Genetics (16 January 2005)
    by Tim Massingham, Nick Goldman
    posted to paml by BioNica on 2006-09-29 12:28:23 as ** along with 4 people and 1 group stevanspringer operon Natasha gjuggler FAB-lab
  • Accuracy and Power of Statistical Methods for Detecting Adaptive Evolution in Protein Coding Sequences and for Identifying Positively Selected Sites
    Genetics, Vol. 168, No. 2. (1 October 2004), pp. 1041-1051.
    by Wendy S Wong, Ziheng Yang, Nick Goldman, Rasmus Nielsen
    posted to paml selection simulations by BioNica on 2006-09-29 12:30:28 as read along with 4 people Natasha timflutre gjuggler CharlesM
  • Statistical methods for detecting molecular adaptation
    Trends in Ecology & Evolution, Vol. 15, No. 12. (1 December 2000), pp. 496-503.
    by Ziheng Yang, Joseph P Bielawski
    posted to paml selection by BioNica on 2006-09-29 12:30:11 as **
  • The power of phylogenetic comparison in revealing protein function.
    Proc Natl Acad Sci U S A (22 February 2005)
    by Ziheng Yang
    posted to paml selection by BioNica on 2006-09-29 12:46:12 as read along with 5 people and 1 group mdimmic stevanspringer bpb tale bpcusack FAB-lab
  • Positive selection driving diversification in plant secondary metabolism
    PNAS, Vol. 103, No. 24. (13 June 2006), pp. 9118-9123.
    by Markus Benderoth, Susanne Textor, Aaron J Windsor, Thomas Mitchell-Olds, Jonathan Gershenzon, Juergen Kroymann
    posted to paml by BioNica on 2006-09-29 12:20:36 as ** along with 1 person and 1 group cmm FAB-lab
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