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HPC Proposal
Brant Faircloth edited this page Nov 30, 2018
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We will be running ExaML, ExaBayes, RAxML, and Astral, among other programs. Each are optimized for MPI and/or run using GNU parallel (ASTRAL, ASTRID):
ExaML (https://sco.h-its.org/exelixis/web/software/examl/)
ExaBayes (https://sco.h-its.org/exelixis/web/software/exabayes/)
RAxML (https://sco.h-its.org/exelixis/web/software/raxml/index.html)
ASTRAL (https://github.com/smirarab/ASTRAL)
ASTRID (https://github.com/pranjalv123/ASTRID)
BEAST (http://beast.bio.ed.ac.uk/)
BioGeoBears (http://phylo.wikidot.com/biogeobears)
RevBayes (https://github.com/revbayes/revbayes)
MCMCtree (http://abacus.gene.ucl.ac.uk/software/paml.html)
PhyloBayes (http://megasun.bch.umontreal.ca/People/lartillot/www/downloadmpi.html)
openmpi-1.6.2-gcc-4.7.2
CPU Range: 1-480. The upper end of the range will be used for the ExaML, ExaBayes, and RAxML programs.
Scaling characteristics of ExaML, ExaBayes, RAxML, ASTRAL, and ASTRID are available from:
ExaML: https://doi.org/10.1093/bioinformatics/btv184
ExaBayes: https://doi.org/10.1093/molbev/msu236
RAxML: https://doi.org/10.1093/bioinformatics/btu033
ASTRAL: https://doi.org/10.1093/bioinformatics/btv234
ASTRID: https://doi.org/10.1186/1471-2164-16-S10-S3
BEAST: https://doi.org/10.1093/molbev/mss075
In review
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BC Faircloth, F Alda, K Hoekzma, MD Burns, C Oliveira, JS Albert, BF Melo, LE Ochoa, FF Roxo, P Chakrabarty, BL Sidlauskas, ME Alfaro. A target enrichment bait set for study- ing relationships among ostariophysan fishes. Methods in Ecology and Evolution. bioRxiv: 10.1101/432583.
CH Oliveros, DJ Field, DT Ksepka, FK Barker, A Aleixo, MJ Andersen, P Alström, BW Benz, EL Braun, MJ Braun, GA Bravo, RT Brumfield, RT Chesser, S Claramunt, J Cracraft, AM Cuervo, EP Derryberry, TC Glenn, MG Harvey, PA Hosner, L Joseph, R Kimball, AL Mack, CM Miskelly, AT Peterson, MB Robbins, FH Sheldon, LF Silveira, BT Smith, ND White, RG Moyle, BC Faircloth. Earth history and the passerine superradiation. Proceedings of the National Academy of Sciences U S A.
Published/Accepted
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F Alda, V Tagliacollo, M Bernt, B Waltz, W Ludt, BC Faircloth, ME Alfaro, J Albert, P Chakrabarty. In press. Resolving deep nodes in an ancient radiation of neotropical fishes in the presence of conflicting signals from incomplete lineage sorting. Systematic Biology.
MW Henson, VC Lanclos, BC Faircloth, JC Thrash. Cultivation and genomics of the first freshwater SAR11 (LD12) isolate. ISME Journal 12:1846–1860. pmid: 29599519 doi: 10.1038/s41396-018-0092-2.
JA Esselstyn, CH Oliveros, MT Swanson, BC Faircloth (2017). Investigating difficult nodes in the placental mammal tree with expanded taxon sampling and thousands of ultraconserved elements. Genome Biol Evol 9:2308–2321. doi: 10.1093/gbe/evx168
ME Alfaro, BC Faircloth, RC Harrington, L Sorenson, M Friedman, CE Thacker, and TJ Near (2018). Explosive diversification of marine fishes at the Cretaceous-Paleogene boundary.. Nature Ecol Evol. doi: 10.1038/s41559-018-0494-6
BC Faircloth. Identifying conserved genomic elements and designing universal probe sets to enrich them. Methods Ecol Evol. doi: 10.1111/2041-210X.12754.
P Chakrabarty, BC Faircloth, CD McMahan, WB Ludt, WL Fink, TJ Near, A Dornberg, JS Albert, J Arroyave, MLJ Stiassny, L Sorenson, ME Alfaro†. Comparative systematics of Ostariophysan fishes with a focus on the perplexing characins (Ostariophysi: Characiformes) using ultraconserved elements, traditional genes, and morphology. Syst Biol. doi:10.1093/sysbio/syx038.
RC Harrington, BC Faircloth, RI Eytan, WL Smith, TJ Near, ME Alfaro, M Friedman. 2016. Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye. BMC Evol Biol 7:12709. pmid: 27769164 doi: 10.1186/s12862-016-0786-x
RG Moyle, CH Oliveros, MJ Andersen, PA Hosner, BW Benz, JD Manthey, SL Travers, RM Brown, BC Faircloth. 2016. Tectonic collision and uplift of Wallacea triggered the global songbird radiation. Nat Commun 7:12709. pmid: 27575437 doi: 10.1038/ncomms12709
MG Harvey, BT Smith, TC Glenn, BC Faircloth, RT Brumfield. 2016. Sequence capture versus restriction site associated DNA sequencing for shallow systematics. Syst Biol 65:910-924. pmid: 27288477 doi: 10.1093/sysbio/syw036.
RW Bryson Jr., BC Faircloth, WLE Tsai, JE McCormack, J Klicka. 2016. Target enrichment of thousands of ultraconserved elements sheds new light on early relationships within New World sparrows (Aves: Passerellidae). Auk 133:451-458. doi: 10.1642/AUK-16-26.1.
MD McGee, BC Faircloth, SR Borstein, J Zheng, CD Hulsey, PC Wainwright, ME Alfaro. 2016. Replicated divergence in cichlid radiations mirrors a major vertebrate innovation. Proc Roy Soc B 283: 20151413. pmid: 26763694 doi: 10.1098/rspb.2015.1413.
NSF DEB-1655624. Awarded. Collaborative Research: All Birds: A Time-scaled Avian Tree From Integrated Phylogenomic and Fossil Data. LSU OSP Proposal #44798 - 1
NSF IOS-1754417. Awarded. Collaborative Research: Enhancers and the con- vergent evolution of limb reduction in squamates. LSU OSP Proposal #46220 - 1