1. Which BLAST? Program Input Database blastn nt nt blastp aa aa blastx nt aa tblastn aa nt tblastx nt nt

2. Seq 1 Seq 2 Seq 3 Seq 4 Seq 1 ATATGATTAG Seq 2 ATATCCTTAG Seq 3 ATAGCCCTAG Seq 4 GGAGCCCTAG ? Phylip Paup MEGA (Molecular evolutionary genetic analysis) Mr. Bayes

3. Alignments Seq 1 ATATGATTAG Seq 2 ATATCCTTAG Seq 3 ATAGCCCTAG Seq 4 GGAGCCCTAG Methods--manual vs automatic (clustal) Programs for data visualization/storage BIOedit, Seq -all, ARB How do I know if it is right? Do I have to use all positions? No--Phylip ---use weights Paup (define character set, can then exclude)

4. Phylogeny packages Phylip---free modular design--suite of different programs that work together example-- dnadist + fitch or seqboot +dnadist + fitch pros--modularity helps conceptualize distinct steps, easy to incorporate into other packages Cons--annoying Paup--not free, (but not too pricey ~$100) single program with options example--use settings to determine distance model, and algorithm/optimality criterion type, then “find tree” command line version enables batch mode MEGA--free, single program, multiple search types Mr. Bayes, free, Bayesian analysis only

5. Overview of lab Sequence from Lab 1 BLAST Alignment Paup Distance, Parsimony, ML tree Phylip Distance tree Treeview ***All tree searches will take some time, so be patient and make sure you have chosen all the right parameters before you execute your searches.