RASP 4 – Reconstruct Ancestral State in Phylogenies

RASP 4

:: DESCRIPTION

RASP is a tool for inferring ancestral state using S-DIVA (Statistical dispersal-vicariance analysis), Lagrange (DEC), Bayes-Lagrange (S-DEC), BayArea, BBM (Bayesian Binary MCMC), BayesTraits and ChromEvol.

::DEVELOPER

Yan Yu

:: SCREENSHOTS

:: REQUIREMENTS

Linux / MacOsX / Windows

:: DOWNLOAD

RASP

:: MORE INFORMATION

Citation

S-DIVA (Statistical Dispersal-Vicariance Analysis): A tool for inferring biogeographic histories.
Yu Y, Harris AJ, He X.
Mol Phylogenet Evol. 2010 Aug;56(2):848-50. doi: 10.1016/j.ympev.2010.04.011

RASP (Reconstruct Ancestral State in Phylogenies): A tool for historical biogeography.
Yu Y, Harris AJ, Blair C, He X.
Mol Phylogenet Evol. 2015 Mar 26;87:46-49. doi: 10.1016/j.ympev.2015.03.008.

RASP 1.0.1 / WebRASP – Assessing the Stability of RNA Structures

RASP 1.0.1 / WebRASP

:: DESCRIPTION

RASP (Ribonucleic Acids Statistical Potential) is a knowledge-based potential for scoring RNA structures based on distance-dependent pairwise atomic interactions.

WebRASP is a server that computes energy scores for assessing the stability of RNA structures. The server receives as input a PDB file containing the atomic coordinates of the RNA structure and calculates the energy profile and total energy score of the molecule. The server displays the results graphically and the visualization can be modified by the user interactively.

::DEVELOPER

Francisco Melo Ledermann

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/ MacOsX
C++ Compiler

:: DOWNLOAD

RASP

:: MORE INFORMATION

Citation

Capriotti E, Norambuena T, Marti-Renom MA, Melo F. (2011)
All-atom knowledge-based potential for RNA structure prediction and assessment.
Bioinformatics 27(8):1086-93

Bioinformatics. 2013 Oct 15;29(20):2649-50. doi: 10.1093/bioinformatics/btt441. Epub 2013 Aug 7.
WebRASP: a server for computing energy scores to assess the accuracy and stability of RNA 3D structures.
Norambuena T1, Cares JF, Capriotti E, Melo F.

RASP 1.90 – RApid Side-chain Predictor

RASP 1.90

:: DESCRIPTION

RASP is a RApid Side-chain Predictor. To achieve a much faster speed with a comparable accuracy to the best existing methods, the authors not only employ the clash elimination strategy of CIS-RR, but also carefully optimize energy terms and integrate different search algorithms. In comprehensive benchmark testings, RASP is over one order of magnitude faster (~ 40 times over CIS-RR) than the recently developed methods, while achieving comparable or even better accuracy.

::DEVELOPER

Zhichao (Chichau) MIAO

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

RASP

:: MORE INFORMATION

Citation:

Zhichao Miao,Yang Cao, Taijiao Jiang 2011
RASP:Rapid modeling of protein side-chain conformations
Bioinformatics (2011) 27 (22): 3117-3122.