:: DESCRIPTION
RECONSTRUCT is a command line program for reconstruction of protein contact maps that uses the distgeom program of the TINKER package.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Optimal contact definition for reconstruction of Contact Maps.
Jose M Duarte, Rajagopal Sathyapriya, Henning Stehr, Ioannis Filippis and Michael Lappe.
BMC Bioinformatics 2010, 11:283.
:: DESCRIPTION
Rast2Systrip reconstructed metabolic networks, and then view the network comparison in Systrip–a Tulip extension. In Systrip, bioinformaticians and biologists can then graphically explore the differences and similarities–side-by-side–in the networks from all levels–globally, from pathways, or between individual metabolites and enzymes.
::DEVELOPER
the Bordeaux Bioinformatics Center
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
DTscore is a distance based tamdem duplication tree reconstruction algorithm. It is based on a simple tandem duplication model, which assumes unequal recombination (crossover) as the only duplication mechanism. All it takes as input is a distance matrix between copies. In this matrix, the rows and columns need to be ordered in the same way as the copies are ordered on the locus. DTscore can be applied to relatively large datasets (more than a hundred copies). Distances can be calculated using programs such as DNADIST (nucleotide sequences) or PROTDIST (protein sequences) from the PHYLIP package. Heterogeneous rates of substitution among sites can be dealt with using the GAMMA method, for example.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Elemento O. and Gascuel O.
An efficient and accurate distance based algorithm to reconstruct tandem duplication trees.
Bioinformatics. 2002 18 :S92-S99.
:: DESCRIPTION
BiRW (Bi-Random Walk)is an algorithm to capture the CBG patterns in the networks for unveiling the associations between the complete collection of disease phenotypes (phenome) and genes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
MaoQiang Xie, TaeHyun Hwang and Rui Kuang
Reconstructing Disease Phenome-genome Association by Bi-Random Walk
Bioinformatics (2012)doi: 10.1093/bioinformatics/bts06
:: DESCRIPTION
REAGO is an assembly tool for 16S ribosomal RNA recovery from metagenomic data
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Reconstructing 16S rRNA genes in metagenomic data.
Yuan C, Lei J, Cole J, Sun Y.
Bioinformatics. 2015 Jun 15;31(12):i35-i43. doi: 10.1093/bioinformatics/btv231.
:: DESCRIPTION
BitPhylogeny is a probabilistic framework to reconstruct intra-tumor evolutionary pathways.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Biol. 2015 Feb 13;16:36. doi: 10.1186/s13059-015-0592-6.
BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies.
Yuan K, Sakoparnig T, Markowetz F, Beerenwinkel N.
:: DESCRIPTION
InferCars is a software of reconstructing contiguous regions of an ancestral genome.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Res. 2006 Dec;16(12):1557-65. Epub 2006 Sep 18.
Reconstructing contiguous regions of an ancestral genome.
Ma J, Zhang L, Suh BB, Raney BJ, Burhans RC, Kent WJ, Blanchette M, Haussler D, Miller W.
:: DESCRIPTION
The purpose of vPhyloMM is to generate a transition model showing the mutational pathways of drug resistance for viruses under drug pressure.
::DEVELOPER
Bioinformatics Research Group (BioRG)
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Buendia, P., Cadwallader, B. and DeGruttola, V. (2009)
A phylogenetic and Markov model approach for the reconstruction of mutational pathways of drug resistance.
Bioinformatics. 2009 Oct 1;25(19):2522-9. doi: 10.1093/bioinformatics/btp466.
:: DESCRIPTION
PhyloQuart is a collection of programs aimed at estimating phylogenies from a quartet principle.
::DEVELOPER
Vincent Berry, and David Bryant
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Vincent Berry, and David Bryant
Faster reliable phylogenetic analysis.
RECOMB (1999) , p. 59-68.
