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RASP specifications

Information


Unique identifier OMICS_13158
Name RASP
Alternative name Reconstruct Ancestral State in Phylogenies
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data Trees datasets
Input format TRE, T, TREES
Output data Biogeographic reconstructions, probabilities of ancestral states at nodes
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Advanced
Version 3.2
Stability Stable
Requirements
Net framework or Wineskin or Mono runtime/Mono-vbnc
Maintained Yes

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Maintainer


  • person_outline Xingjin He

Publication for Reconstruct Ancestral State in Phylogenies

RASP citations

 (88)
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Shifts in diversification rates and host jump frequencies shaped the diversity of host range among Sclerotiniaceae fungal plant pathogens

2018
Mol Ecol
PMCID: 5900718
PMID: 29421852
DOI: 10.1111/mec.14523
call_split See protocol

[…] To infer possible ancestral hosts, we used Reconstruct Ancestral State in Phylogenies 3.1 (RASP) (Yu, Harris, Blair, & He, ). We used the S‐DIVA (Statistical Dispersal‐Vicariance Analysis), S‐DEC (Statistical Dispersal–Extinction–Cladogenesis […]

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Ancient Evolution of Mammarenaviruses: Adaptation via Changes in the L Protein and No Evidence for Host–Virus Codivergence

2018
Genome Biol Evol
PMCID: 5863214
PMID: 29608723
DOI: 10.1093/gbe/evy050
call_split See protocol

[…] mmarenavirus phylogeny were obtained using the discrete model () implemented in BEAST (version 2.4.4) ().Geographic origin was also inferred using the BBM (Bayesian Binary MCMC) method implemented in RASP (Reconstruct Ancestral State in Phylogenies) (; ).BEAST analyses were performed using the Bayesian Markov Chain Monte Carlo (MCMC) method with a General Time Reversible (GTR) substitution model a […]

call_split

Origin and dispersal of Hepatitis E virus

2018
PMCID: 5837148
PMID: 29410449
DOI: 10.1038/s41426-017-0009-6
call_split See protocol

[…] ees were visualized with FigTree (http://tree.bio.ed.ac.uk/).Both ancestral characters (geographic origin and host range) were also inferred using the BBM (Bayesian Binary MCMC) method implemented in RASP (Reconstruct Ancestral State in Phylogenies), . For BBM analyses, 10 000 BEAST-generated trees and consensus tree were used as topology input. Two BBM chains were run for 100 000 generation with […]

call_split

Molecular Phylogeny and Dating of Forsythieae (Oleaceae) Provide Insight into the Miocene History of Eurasian Temperate Shrubs

2018
Front Plant Sci
PMCID: 5807412
PMID: 29459880
DOI: 10.3389/fpls.2018.00099
call_split See protocol

[…] tion. The ancestral area reconstruction and the estimation of the spatial patterns of geographic diversification within Forsythieae were inferred using the Bayesian binary method (BBM) implemented in Reconstruct Ancestral State in Phylogenies (RASP) v.3.0 (). The BBM was selected for its tendency to suggest single distribution areas for ancestral nodes compared to others and capability of providin […]

library_books

Origins and biogeography of the Anolis crassulus subgroup (Squamata: Dactyloidae) in the highlands of Nuclear Central America

2017
BMC Evol Biol
PMCID: 5740896
PMID: 29268694
DOI: 10.1186/s12862-017-1115-8

[…] To infer the ancestral distribution of the Anolis crassulus subgroup, we conducted ancestral area reconstruction using a Bayesian Binary Markov-chain Monte Carlo (BBM) [] analysis implemented in RASP v3.2 [] using the post burn-in trees obtained from BEAST to account for phylogenetic uncertainty. This method statistically infers an ancestral state at a node by averaging its frequency across a […]

library_books

Long‐distance dispersal or postglacial contraction? Insights into disjunction between Himalaya–Hengduan Mountains and Taiwan in a cold‐adapted herbaceous genus, Triplostegia

2017
Ecol Evol
PMCID: 5773327
PMID: 29375785
DOI: 10.1002/ece3.3719

[…] We used the Bayesian Binary MCMC (BBM) method implemented in RASP 3.0.0 to estimate the possible ancestral areas of Triplostegia with the trees obtained from the intraspecific BEAST analysis (Yu, Harris, Blair, & He, ). Three geographical regions that represent […]

Citations

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RASP institution(s)
Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China; Department of Biology, Duke University, Durham, NC, USA; Department of Botany, Oklahoma State University, Stillwater, OK, USA; Department of Biological Sciences, New York City College of Technology, New York, NY, USA
RASP funding source(s)
National Natural Science Foundation of China (Grant Nos. 31270241, 31100161); the Specimen Platform of China, Teaching Specimen’s sub-platform

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