Phylogenetic Analysis Dayong Guo

Introduction Phylogenetics is the study of evolutionary relatedness among various species, populations, or among a set of sequences. Besides the study of morphology or phenotype with traditional definitions and concepts, molecular analysis with modern computational tools has shown their unique strength in phylogenetics since the DNA, RNA or protein sequence data are naturally discretely defined. Several computational algorithms have been developed to build phylogenetic trees with the input of multiple sequences. The most commonly used types of algorithms include distance-matrix methods (e.g. neighbor-joining), maximum parsimony, maximum likelihood and Bayesian inference, etc. The PHYLIP (PHYLogeny Inference Package, Felsenstein) is one of the most popular tools for phylogenetic analysis. It includes parsimony, distance matrix and likelihood methods.

Method and Tool Datasets 1)Four artificially made, short and simple sequences (textbook page 303) 2)Four real protein sequences (Bone Morphogenetic Protein 2 from human, mouse, rat and frog) Tools 1)Use ClustalW as the aligment generator. 2)Use PHYLIP to generate phylogenetic trees (distance method, parsimony method)

Results 1 From distance method (Fitch-Margoliash algorithm) From parsimony method (Detailed processes not shown) Alignment by CLUSTALW 4 20 SeqC ACGCATTGAA TGATGATAAT SeqD ACACATTGAG TGATAATAAT SeqA ACGCGTTGGG CGATGGCAAC SeqB ACGCGTTGGG CGACGGTAAT

Result 2 1)Four sequences of BMP2BMP2 2)Alignment generated by CLUSTALWCLUSTALW 3)Download PHYLIP and installPHYLIP 4)Use protdist.exe  fitch.exe as an example of distance method; Or, use protpars.exe as an example of parsimony method 5)Drawtree.exe

Discussion Distance tree and parsimony tree are different for the BMP2 dataset. It could be result from relatively lower homology btw frog and other species. Distance tree Parsimony tree

Discussion (cont) The PHYLIP program set includes multiple algorithms and options providing convenience and flexibility. And, different versions enable performance on various OS platforms. However, the text-based interface is not friendly. And, there is no online service.