INTRODUCTION

RASP (Reconstruct Ancestral State in Phylogenies) is a tool for inferring ancestral state using S-DIVA (Statistical dispersal-vicariance analysis), Lagrange (DEC), Bayes-Lagrange (S-DEC), BayArea and BBM (Bayesian Binary MCMC) method.

Note: A manuscript describing the RASP program has been submitted. Please cite the manuscript after it has been published. In the meantime, please cite the program and our pervious paper.

New RASP v 3.0 for Windows and Mac OS X has been released! Two new methods have been added to RASP: Bayes-Lagrange and BayArea. The new version of RASP are faster than ever!
Please don't hesitate to mail me (sculab@gmail.com) if you have any questions.
Last update: 09/15/2014

DOWNLOAD

Source Code (For Developers):
Most users should NOT download these:
Main programme (VB 2010):
RASP (v3.0)
Library (VC 2010):
BAYESDLL is modified from source code of Mrbayes
CONSDLL and PARSDLL are modified from source code of PHYLIP
DIVADLL is modified from source code of DIVA 1.2
LAGDLL is modified from source code of Lagrange C++ Version
BAYAREADLL is modified from source code of BAYAREA
Command Line Tools (VC 2010):
Lagrange_Win is modified from source code of Lagrange C++ Version
BAYAREA is modified from source code of BAYAREA


Windows:
Download the archive from following:
RASP for Win (v3.0, 20140915)
Run “RASP.exe” to load the program.

System Requirement:
If you are using Windows 2000, 2003 or XP, please make sure that Microsoft® .NET 2 Framework is installed on your computer. This is usually installed through Windows updates, but it may be absent from older systems. The .NET framework 2 packages are available for free here and should be installed prior to using RASP.


Mac OS:
Download the archive from following:
RASP for Mac (v3.0, 20140915)
Run “RASP” to load the program.

System Requirement:
This version of RASP is developed for use on Mac OS X versions 10.6 and above on computers with Intel processors only. RASP for Mac uses the Wineskin program in order for RASP to run.

Linux:
There are very few people using the Linux version of RASP, so we will not update the old version of RASP for Linux.
For Linux users, one could use Wine and Winetricks to run RASP for Win (recommended). Using following command to install Winesticks and .NET framework:
wget http://kegel.com/wine/winetricks
sh winetricks dotnet20

Important: Please use "Root Terminal" to run RASP and RASP must be loaded in it's own folder. For instance:
Change the dictionary to RASP's folder: 'cd /home/user/Desktop/RASP_Win'
Run RASP: './RASP.exe'

You could also download the old version of RASP for Linux (Not recommended):
RASP for Linux (v2.0b, 20120319)
Run “RASP_linux.sh” to load the program.

System Requirement:
You need Mono runtime (Recommend version 2.6.7) and Mono-vbnc to run RASP. Mono is a software platform designed to allow developers to easily create cross platform applications. The Mono Framework packages are available for free here.
For Ubuntu 10.x and Debian 6.x users: Mono runtime have already installed in ubuntu. You may simply use “sudo apt-get install mono-vbnc” to install Mono-vbnc.

CITATION

The BBM and time-events curve algorithms have been described in Yu et al. (2014, submitted). If you are using the S-DIVA method, you may also want to cite Yu et al. (2010).

Before our manuscript is published, you could cite the program and website:
Yu Y, Harris AJ, He XJ. S-DIVA (Statistical Dispersal-Vicariance Analysis): a tool for inferring biogeographic histories. Molecular Phylogenetics and Evolution. 56: 848-850
Yu Y, Harris AJ, He X-J. 2014. RASP (Reconstruct Ancestral State in Phylogenies) 3.0. Available at http://mnh.scu.edu.cn/soft/blog/RASP

Some Articles using RASP (S-DIVA)

Tavera J.J, Acero A.P,Balart E.F. and G Bernardi. 2012. Molecular phylogeny of grunts (Teleostei, Haemulidae), with an emphasis on the ecology, evolution, and speciation history of New World species. BMC Evolutionary Biology 2012, 12:57
Calvente A, Zappi D C, Forest F, et al. 2011. Molecular Phylogeny, Evolution, and Biogeography of South American Epiphytic Cacti. International Journal of Plant Sciences. DOI: 10.1086/660881
Antonelli, A, Verola CF, Parisod C, Gustafsson ALS. 2010. Climate cooling promoted the expansion and radiation of a threatened group of South American orchids (Epidendroideae:Laeliinae). Biological Journal of the Linnean Society. 100(3):596-606
Jestrow B, Gutiérrez Amaro J, Francisco‐Ortega J. Islands within islands: a molecular phylogenetic study of the Leucocroton alliance (Euphorbiaceae) across the Caribbean Islands and within the serpentinite archipelago of Cuba[J]. Journal of Biogeography, 2012, 39(3): 452-464.
Thomas D C, Hughes M, Phutthai T, et al. West to east dispersal and subsequent rapid diversification of the mega‐diverse genus Begonia (Begoniaceae) in the Malesian archipelago[J]. Journal of Biogeography, 2012, 39(1): 98-113.
Fernandez-Mazuecos M, Vargas P. Historical isolation versus recent long-distance connections between Europe and Africa in bifid toadflaxes (Linaria sect. Versicolores)[J]. PloS one, 2011, 6(7): e22234.
Hou Z, Sket B, Fi?er C, et al. Eocene habitat shift from saline to freshwater promoted Tethyan amphipod diversification[J]. Proceedings of the National Academy of Sciences, 2011, 108(35): 14533-14538.
CHAVES J A, WEIR J T, SMITH T B. Diversification in Adelomyia hummingbirds follows Andean uplift. Molecular Ecology, 2011.
Jason T. Weir, Momoko Price. 2011. Andean uplift promotes lowland speciation through vicariance and dispersal in Dendrocincla woodcreepers. Molecular Ecology. 20(21):4550-4563
Jessica R. Litman, Bryan N. Danforth, Connal D. Eardley and Christophe J. Praz. 2011. Why do leafcutter bees cut leaves? New insights into the early evolution of bees. Proceedings of the Royal Society B: Biological Sciences. doi: 10.1098/rspb.2011.0365
Li, Q.-Q., Zhou, S.-D., He, X.-J., Yu, Y., Zhang, Y.-C., Wei, X.-Q. 2010. Phylogeny and biogeography of allium (Amaryllidaceae: Allieae) based on nuclear ribosomal internal transcribed spacer and chloroplast rps16 sequences, focusing on the inclusion of species endemic to China . Annals of Botany. 106(5):709-733
Linlin Zhou, Yvonne C. F. Su, Daniel C. Thomas, Richard M. K. Saunders. 2011. "Out-of-Africa" dispersal of tropical floras during the Miocene climatic optimum: evidence from Uvaria (Annonaceae). Journal of Biogeography. DOI: 10.1111/j.1365-2699.2011.02598.x
Morales-Hojas, R., Reis, M., Vieira, C.P., Vieira, J. 2011. Resolving the phylogenetic relationships and evolutionary history of the Drosophila virilis group using multilocus data . Molecular Phylogenetics and Evolution. 60(2):249-258
Ocampo, G., Columbus, J.T. 2010. Molecular phylogenetics of suborder Cactineae (Caryophyllales), including insights into photosynthetic diversification and historical biogeography . American Journal of Botany. 97(11):1827-1847
Razo-Mendivil U, Pérez-Ponce de León G. Testing the evolutionary and biogeographical history of< i> Glypthelmins(Digenea: Plagiorchiida), a parasite of anurans, through a simultaneous analysis of molecular and morphological data[J]. Molecular phylogenetics and evolution, 2011, 59(2): 331-341.
Scott Zona, Javier Francisco-Ortega, Brett Jestrow, William J. Baker and Carl E. Lewis. 2011. Molecular phylogenetics of the palm subtribe Ptychospermatinae (Arecaceae). American Journal of Botany. doi: 10.3732/ajb.1100218
Shujait Ali, Yan Yu, Martin Pfosser, and Wolfgang Wetschnig. 2011. Inferences of biogeographical histories within subfamily Hyacinthoideae using S-DIVA and Bayesian binary MCMC analysis implemented in RASP (Reconstruct Ancestral State in Phylogenies). Annals of Botany. doi:10.1093/aob/mcr274
Strijk JS, Noyes RD, Strasberg D, Cruaud C, Gavory F, et al. (2012) In and out of Madagascar: Dispersal to Peripheral Islands, Insular Speciation and Diversification of Indian Ocean Daisy Trees (Psiadia, Asteraceae). PLoS ONE 7(8): e42932. doi:10.1371/journal.pone.0042932
Subbotin, S.A., Prado Vera, I.C.D., Mundo-Ocampo, M., Baldwin, J.G. 2011. Identification, phylogeny and phylogeography of circumfenestrate cyst nematodes (Nematoda: Heteroderidae) as inferred from analysis of ITS-rDNA . Nematology. 13(7):805-824
Thiv, M., van der Niet, T., Rutschmann, F., Thulin, M., Brune, T., Linder, H.P. 2011. Old-New World and trans-African disjunctions of Thamnosma (Rutaceae): Intercontinental long-distance dispersal and local differentiation in the succulent biome . American Journal of Botany. 98(1):76-87
Thomas J. Givnish, Michael H. J. Barfuss, Benjamin Van Ee et al. 2011. Phylogeny, adaptive radiation, and historical biogeography in Bromeliaceae: Insights from an eight-locus plastid phylogeny. American Journal of Botany. 98(5):872-895
Yu, Y., Downie, S.R., He, X-J, Deng, X-L, Yan, L. 2011. Phylogeny and biogeography of Chinese Heracleum (Apiaceae tribe Tordylieae) with comments on their fruit morphology . Plant Systematics and Evolution. 296(3-4):179-203
Yu, Y., Harris AJ, He X-J. 2010. S-DIVA (Statistical Dispersal-Vicariance Analysis): a tool for inferring biogeographic histories. Molecular Phylogenetics and Evolution. 56: 848-C850