Phylogenetic Workflows: Tree Building and Post-tree Analyses Given at the Dept for Ecology and Evolutionary Biology, University of Arizona in 2011 A phylogenetic workflow example showcasing iPlant Cyberinfrastructure

1. Phylogenetic Workflows: Tree Building and Post-tree Analyses Naim Matasci The iPlant Collaborative Plant Biology 2011 August 6-10, 2011

2. Why is the tree of life important? “ Knowledge of evolutionary relationships is fundamental to biology, yielding new insights across the plant sciences, from comparative genomics and molecular evolution, to plant development, to the study of adaptation, speciation, community assembly, and ecosystem functioning.”

3. Nothing in biology makes sense except in the light of evolution. T. G. Dobzahnsky

4. Scalability Ackerly, 2009; J. Felsenstein, ca. 1980; Ranger Cluster at TACC

6. Ancestral state of Hawaiian lobelioids Lobelia niihauensis (Image: David Eickhoff) Cyanea leptostegia (Image: Karl Magnacca)

8. Continuous Ancestral Character Estimation (Schulter et al. 1997, Paradis 2004) ?

11. >gi|1835233|emb|Z83147.1| S.nepaulensis rbcL gene TTATTATACTCCTGAATAYGAAACCAAAGATACTGATATCTTGGCAGCATTCCGAGTAACTGCTCAGCCT GGAGTTCCACCCGAAGAAGCGGGGGCCGCGGTAGCTGCGGAATCTTCTACTGGTACATGGACAACTGTGT GGACCGATGGACTTACTAACCTTGATCGTTACAAAGGGCGATGCTACAACATAGAGCCCGTTGCTGGAGA AGAAAATCAATTTATTGCTTATGTAGCTTATCCTTTAGACCTTTTTGAAGAAGGTTCTGTTACTAACATG TTTACTTCCATTGTGGGTAATGTATTTGGGTTCAAAGCCCTGCGCGCTCTACGTCTGGAAGATCTGCGAA TCCCTACTGCGTATTGTAAAACTTTCCAAGGACCGCCTCATGGGATCCAAGTTGAAAGAGATAAATTGAA CAAGTATGGTCGTCCCTTGCTGGGATGTACTATTAAACCTAAATTGGGGTTATCGGCTAAAAACTACGGT AGAGCAGTTTATGAATGTCTACGCGGTGGGCTTGATTTTACCAAAGATGATGAGAACGTGAACTCCCAAC CATTTATGCGTTGGAGAGACCGTTTCGTATTTTGTGCCGAAGCAATTTTTAAAGCACAGTCTGAAACAGG TGAAATCAAAGGGCATTACTTGAATGCTACTGCAGGTACATGTGAAGAAATGATGAAAAGGGCTATATTT >gi|1835227|emb|Z83136.1| S.foetidissimum rbcL gene AAGTGTTGGATTCAAAGCGGGTGTTAAAGATTACAAATTGACTTATTATACTCCTGACTATGAAACCAAA GATACTGATATCTTGGCAGCATTCCGAGTAACTCCTCAACCTGGAGTTCCACCTGAAGAAGCAGGGGCCG CGGTAGCTGCCGAATCTTCTACTGGTACATGGACAACTGTGTGGACCGATGGACTTACTAGCCTTGATCG TTACAAAGGGCGATGCTACCACATCGAGCCCGTNGCTGGAGAAGAAAATCAATATATTGCTTATGTAGCT TATCCTTTAGACCTYTTTGAAGAAGGTTCTGTTACTAATATGTKNACTTCCATTGTGGGGAATGTATTTG GGTTCAAAGCCCTGCGTGCTTTACGTCTGGAAGATCTGCGAATCCCTCCTGCGTATTCTAAAACTTTCCA AGGACCGCCTCATGGCATCCAAGTTGAAAGAGATAAATTGAACAAGTACGGTCGTCCCCTGTTGGGATGT ACTATTAAACCTAAATTGGGGTTATCTGCTAAAAACTACGGTAGAGCGGTTTATGAATGTCTCCGCGGTG GACTTGATTTTACCAAAGATGATGAGAACGTGAACTCCCAACCATTTATGCGTTGGAGAGATCGTTTCTT ATTTTGTGCCGAAGCACTTTATAAAGCACAGGCTGAAACAGGTGAAATCAAAGGGCATTACTTGAATGCT >gi|1834456|emb|Z83132.1| G.urceolata rbcL gene AACTAAAGCGGGTGTTGGATTCAAAGCGGGTGTTAAAGATTACAAATTAACTTATTATACTCCTGACTAT GAAACCAAAGATACTGATATCTTGGCAGCATTCCGAGTAACTCCTCAACCTGGAGTTCCACCTGAAGAAG CGGGGGCCGCCGTAGCTGCCGAATCCTCCACTGGTACATGGACAACTGTGTGGACCGACGGACTTACTAG CCTTGATCGTTACAAAGGGCGATGCTACCACATCGAGCCCGTGGCTGGAGAAGAAAATCAATTTATTGCT TATGTAGCTTACCCTTTAGACCTTTTTGAAGAAGGTTCTGTTACTAACATGTTTACTTCCATTGTGGGTA ATGTATTTGGGTTCAAAGCCCTGCGCGCTCTACGTCTGGAAGATCTGCGAATCCCTGTTGCGTATGCTAA AACTTTCCAAGGGCCGCCTCATGGCATCCAAGTTGAAAGAGATAAATTGAATAAGTATGGTCGTCCCCTG

13. Get sequences DEMO

23. muscleDEMO

32. RAxML DEMO

41. iPlant Tree Viewer http://portnoy.iplantcollaborative.org/

42. Live tree view demo

50. Obstacles

51. Lopper DEMO

64. Lobelia kauaensis Lobelia villosa Galeatella gloria-montis Trematolobelia kauaiensis Trematolobelia macrostachys Lobelia hypoleuca Neowimmeria yuccoides Lobelia niihauensis Brighamia insignis Brighamia rockii Delissea rhytidosperma Delissea subcordata Cyanea acuminata Cyanea hirtella Cyanea coriacea Delissea leptostegia Clermontia kakeana Clermontia parviflora Clermontia arborescens Clermontia fauriei

65. The TNRS: A Taxonomic Name Resolution Service for Plants Tonight from 5:30 - 7:30 in Exhibit Hall A. Poster number P21011 .

67. CACE DEMO