1. 1. Basic concepts of molecular evolution


  1. 2. Sequence databases and database searching


  1. 3. Multiple sequence alignment


  3. primatesNuc.fasta: mac, windows, unix

  4. primatesAA.fasta: mac, windows, unix


  1. 4. Nucleotide substitution models

  2. Primates.phy: mac, windows, unix

  3. Primates_cdp_categories.phy: mac, windows, unix

  4. primates.fas: windows


  1. 5. Phylogenetic inference based on distance methods

  2. primates.meg: mac, windows, unix

  3. primates.phy: mac, windows, unix

  4. mtDNA.phy: mac, windows, unix


  1. 6. Phylogenetic inference using maximum likelihood methods

  2. hivALN.phy: mac, windows, unix


  1. 7. Bayesian Phylogenetic Analysis Using MrBayes

  2. primates.nex: mac, windows, unix

  3. cynmix.nex: mac, windows, unix


  1. 8. Phylogeny inference based on parsimony and other methods using PAUP*

  2. hivALN.phy: mac, windows, unix

  3. gdp.phy: mac, windows, unix

  4. mtDNA.nex: mac, windows, unix


  1. 9. Phylogenetic analysis using protein sequences

  2. LmjF30.2980.fas

  3. g3pg_leime.fasta

  4. g3pdh.mb: mac, windows, unix


  1. 10. Selecting models of evolution

  2. mtDNA.nex: mac, windows, unix

  3. gpd.phy: mac, windows, unix

  4. PIVenvEd.nex: mac, windows, unix


  1. 11. Molecular clock analysis

  2. baseml.ctl: mac, windows, unix

  3. primates.phy: mac, windows, unix

  4. primates_rooted.tre: mac, windows, unix

  5. primates_unrooted.tre: mac, windows, unix

  6. RSVA.phy: mac, windows, unix

  7. RSVA_dates.phy: mac, windows, unix

  8. RSVA_dates_rooted.tre: mac, windows, unix

  9. RSVA_logN_baySky.xml: mac, windows, unix

  10. RSVA_rooted.tre: mac, windows, unix

  11. RSVA_strict_baySky.xml: mac, windows, unix

  12. RSVA_unrooted.tre: : mac, windows, unix


  1. 12. Testing Tree Topologies

  2. hivALN.phy: mac, windows, unix

  3. hivALN.15trees: mac, windows, unix


  5. 13. Natural selection and adaptation of molecular sequences


  1. 14. Estimating selection pressures on alignments of coding sequences

  2. Data.zip

  3. Results.zip


  1. 15. Introduction to recombination detection


  1. 16. Detecting and characterizing individual recombination events

  2. A-J-cons-kal153.fsa

  3. A-J-cons-recombinants.fsa

  4. 2000-HIV-subtype.fsa


  1. 17. The Coalescent: population genetic inference using genealogies


  1. 18. Bayesian evolutionary analysis by sampling trees

  2. RSVA.nex: mac, windows, unix


  1. 19. LAMARC: Estimating population genetic parameters from molecular data

  2. ward.phy: mac, windows, unix


  1. 20. Assessing substitution saturation with DAMBE

  2. InvertebrateEF1a.fas

  3. SIV.fas

  4. VertebrateMtCOI.fas


  1. 21. Split Networks. A tool for exploring complex evolutionary relationships in molecular data

  2. hivALN.nex: mac, windows, unix

  3. mtDNA.nex: mac, windows, unix

Philippe Lemey

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A Practical Approach to phylogenetic analysis and hypothesis testing

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