1. Methods for Phylogenetics and Evolutionary analysis Jianpeng Xu University of Nebraska-Omah a

2. Phylogeny Phylogeny is the evolutionary history of a species or group of related species. Phylogenetic trees are used to place different taxonomic schemes together, and to show connection between classification and phylogeny. Phylogenetic trees are used to place different taxonomic schemes together, and to show connection between classification and phylogeny. DNA, RNA and protein sequences can be compared to determine phylogeny.

3. Six steps of phylogenetics and evolutionary analysis 1. Obtain Sequence data 2. Multiple sequence alignment 3. Model of substitution 4. Tree-building 5. Tree-visualization 6. Evolutionary analysis

4. Step 1: Obtain DNA, RNA or protein sequences 1.For phylogeny, DNA can be more informative. 2. For phylogeny, protein sequences are also often used. 3. NCBI GenBank is popular for obtaining sequences. http://www.ncbi.nlm.nih.gov/ http://www.ncbi.nlm.nih.gov/

5. Step 2: Multiple sequence alignment 1. The fundamental basis of a phylogenetic tree is a multiple sequence alignment. a multiple sequence alignment. 2. Programs: 1) Muscle (MUltiple Sequence Comparison by Log- Expectation) 1) Muscle (MUltiple Sequence Comparison by Log- Expectation) 2) Mafft(Multiple Alignment using Fast Fourier Transform) 2) Mafft(Multiple Alignment using Fast Fourier Transform) 3) TranslatorX:align protein-coding nucleotide sequences based on their corresponding amino acid translations. 3) TranslatorX:align protein-coding nucleotide sequences based on their corresponding amino acid translations. http://www.ebi.ac.uk/Tools/sequence.html http://www.ebi.ac.uk/Tools/sequence.html http://translatorx.co.uk/ http://translatorx.co.uk/

6. Step 3: Model of substitution 1.Modeltest http://darwin.uvigo.es/software/modeltest_server.html 2. Modelgenerator http://bioinf.may.ie/software/modelgenerator/

7. Step 4: Tree-building methods 1.Distance-based: 1)Neighbor-joining: 1)Neighbor-joining: MEGA: http://www.megasoftware.net/ PAUP: http://paup.csit.fsu.edu/ PAUP: http://paup.csit.fsu.edu/ 2. Character-based: 1) Maximum-parsimony: PAUP, Phylip 1) Maximum-parsimony: PAUP, Phylip 2) Maximum-likelihood: RAxML, Garli 2) Maximum-likelihood: RAxML, Garli 3) Bayesian: MrBayes 3) Bayesian: MrBayes http://www.phylo.org/portal2/login!input.action http://www.phylo.org/portal2/login!input.actionhttp://www.phylo.org/portal2/login!input.action RAxML uses rapid algorithms for bootstrap and maximum likelihood searches and is considered one of the fastest and most accurate phylogeny programs.

8. Step 5: Tree-visualization FigTree: http://tree.bio.ed.ac.uk/software/figtree/ ttp://tree.bio.ed.ac.uk/software/figtree/ Here is the tree of neuraminidase gene of influenza virus

9. Step 6: Evolutionary analysis BEAST package: http://beast.bio.ed.ac.uk/Main_Page http://beast.bio.ed.ac.uk/Main_Pagehttp://beast.bio.ed.ac.uk/Main_Page BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences.