What might you need to improve the tree next time?

352H Bioinformatic Methods Summer2012 ? Lab Report 2 CSB352: Lab Report 2 Objective: Perform a phylogenetic analysis on your subset of BLAST hits from At4g28230 generating the best-resolved phylogenetic tree you can. In addition, perform Datamonkey analysis on the sequence set, and determine what kind of selection (or lack thereof) is acting on the orthologs. Your report should be no more than four pages (at minimum 1.5 line spacing; you are encouraged to print double-sided) and include the following. Figures and references are not included in the page count: -Introduction (1/2 page max): 2 marks Summarize the genes and taxa included in your analysis. As a continuation of the previous lab report, make note of any pertinent alignment patterns you detected last time (ie: conserved regions, range of sequence identity, etc.), and succinctly state what you are therefore trying to do in this subsequent analysis (do not copy the above objective!). -Methods (1/2 page max): 4 marks Briefly describe the multiple sequence alignment used in your analysis. Explain the design of your phylogenetic and selection analysis in prose form, including the software used, the alignment and phylogenetic treebuilding algorithms used (justify your choices), the parameters you chose for each algorithm, and the selection tests done. DO NOT INCLUDE RESULTS IN THIS SECTION (see below.) -Results (~1 page, with tree image): 6 marks A write-up in which the results of your analysis are displayed and described (but not analysed). Include (within this page) your preferred phylogenetic tree with branch lengths and bootstrap values. In the text, explain any pertinent trends, divergences, or similarities seen in your tree. As well, include a summary of the selection test results. -Discussion (~1/2 page): 3 marks Interpret your results ? does your tree make sense in terms of taxonomic clustering? Are there any inconsistencies that surprise you? Is the tree highly resolved and if not, why not? What might you need to improve the tree next time? Also, interpret your selection analysis biologically ? does the type of selection chosen coincide with the function of the orthologs in your analysis, if any could be deduced?