:: DESCRIPTION
ProtASR is an evolutionary framework to reconstruct ancestral protein sequences accounting for structural constraints.
::DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Arenas M, Weber CC, Liberles DA, Bastolla U.
ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability.
Syst Biol. 2017 Nov 1;66(6):1054-1064. doi: 10.1093/sysbio/syw121. PMID: 28057858.
:: DESCRIPTION
GeneNetStudio is a software package developed for visual reconstruction and analysis of network models of molecular-genetic systems.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
GPRuler is an open-source tool to automate the reconstruction process of gene-protein-reaction (GPR) rules for any living organism, which describe with a Boolean logic relationships between the gene products (e.g., enzyme isoforms or subunits) associated with the catalysis of a given reaction.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Di Filippo M, Damiani C, Pescini D.
GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction.
PLoS Comput Biol. 2021 Nov 8;17(11):e1009550. doi: 10.1371/journal.pcbi.1009550. Epub ahead of print. PMID: 34748537.
:: DESCRIPTION
Quikr is a QUadratic, Iterative, K-mer based Reconstruction technique that utilizes sparsity promoting ideas from the field of compressed sensing to reconstruct the composition of a bacterial community (when the input data is 454-like pyrosequencing data).
::DEVELOPER
Mathematical Biosciences Institute, The Ohio State University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing.
Koslicki D, Foucart S, Rosen G.
Bioinformatics. 2013 Sep 1;29(17):2096-102. doi: 10.1093/bioinformatics/btt336.
:: DESCRIPTION
PRT (Pedigree Reconstruction Tools) is a software for the reconstruction of single generation sibling groups (SG). A wider range of enumeration algorithms is included, permitting improved computational performance. In particular, an iterative version of the algorithm designed for larger samples is included in a fully automated form.
::DEVELOPER
Anthony Almudevar, PhD
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mol Ecol Resour. 2012 Jan;12(1):164-78. doi: 10.1111/j.1755-0998.2011.03061.x. Epub 2011 Aug 26.
A new version of PRT software for sibling groups reconstruction with comments regarding several issues in the sibling reconstruction problem.
Almudevar A, Anderson EC.
:: DESCRIPTION
CoReCo is a computational method for reconstructing metabolic networks of multiple species from protein sequence and phylogenetic data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species.
Pitkänen E, Jouhten P, Hou J, Syed MF, Blomberg P, Kludas J, Oja M, Holm L, Penttilä M, Rousu J, Arvas M.
PLoS Comput Biol. 2014 Feb 6;10(2):e1003465. doi: 10.1371/journal.pcbi.1003465.
:: DESCRIPTION
GEMSiRV is a software platform to provide functionalities of easy metabolic network drafting and editing, amenable network visualization for experimental data integration and flux balance analysis tools for simulation studies.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2012 Jul 1;28(13):1752-8. doi: 10.1093/bioinformatics/bts267. Epub 2012 May 4.
GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization.
Liao YC1, Tsai MH, Chen FC, Hsiung CA.
:: DESCRIPTION
novoSpaRc predicts locations of single cells in space by solely using single-cell RNA sequencing data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Moriel N, Senel E, Friedman N, Rajewsky N, Karaiskos N, Nitzan M.
NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport.
Nat Protoc. 2021 Sep;16(9):4177-4200. doi: 10.1038/s41596-021-00573-7. Epub 2021 Aug 4. PMID: 34349282.
:: DESCRIPTION
FASTCORE is a generic algorithm for reconstructing context-specific metabolic network models from global genome-wide metabolic network models such as Recon X.
::DEVELOPER
Life Sciences Research Unit, University of Luxembourg
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS Comput Biol. 2014 Jan;10(1):e1003424. doi: 10.1371/journal.pcbi.1003424. Epub 2014 Jan 16.
Fast reconstruction of compact context-specific metabolic network models.
Vlassis N, Pacheco MP, Sauter T
:: DESCRIPTION
GNTInfer aims to combine computational analysis of multiple microarray datasets and biological experiment results together for inferring gene regulatory network and further identifying compound targets of perturbation experiments.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, and Luonan Chen.
Recovering gene regulation and identifying compound targets by integrating multiple time course expression datasets and prior information.
Manuscript, 2007.
