:: DESCRIPTION
Jane is a software tool for the cophylogeny reconstruction problem.
::DEVELOPER
:: SCREENSHOTS
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Jane: a new tool for the cophylogeny reconstruction problem.
Conow C, Fielder D, Ovadia Y, Libeskind-Hadas R.
Algorithms Mol Biol. 2010 Feb 3;5:16. doi: 10.1186/1748-7188-5-16.
:: DESCRIPTION
PULCHRA (PowerfUL CHain Restoration Algorithm) is a simple command-line tool for all-atom reconstruction and refinement of reduced protein models. PUCLHRA can correct alpha carbon positions, add backbone and side chain atoms, improve hydrogen bonds patterns and check proper protein chirality.
::DEVELOPER
Center for the Study of Systems Biology
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Rotkiewicz P., Skolnick, J.,
Fast procedure for reconstruction of full-atom protein models from reduced representations.
J. Comp. Chem., Jul 15, 29(9), 1460-5 (2008).
:: DESCRIPTION
The RAVEN Toolbox is a complete environment for reconstruction, analysis, simulation, and visualization of GEMs and runs within MATLAB.
:: DEVELOPER
Systems & Synthetic Biology – SYSBIO, Chalmers University of Technology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Wang H, Marcišauskas S, Sánchez BJ, Domenzain I, Hermansson D, Agren R, Nielsen J, Kerkhoven EJ.
RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor.
PLoS Comput Biol. 2018 Oct 18;14(10):e1006541. doi: 10.1371/journal.pcbi.1006541. PMID: 30335785; PMCID: PMC6207324.
PLoS Comput Biol. 2013;9(3):e1002980. doi: 10.1371/journal.pcbi.1002980. Epub 2013 Mar 21.
The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum.
Agren R1, Liu L, Shoaie S, Vongsangnak W, Nookaew I, Nielsen J.
:: DESCRIPTION
TSCAN (Tools for Single-Cell ANalysis) is a software tool developed to better support in silico pseudo-Time reconstruction in Single-Cell RNA-seq ANalysis.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis.
Ji Z, Ji H.
Nucleic Acids Res. 2016 May 13. pii: gkw430.
:: DESCRIPTION
methylFlow is a software of cell-specific methylation pattern reconstruction from high-throughput bisulfite-converted DNA sequencing.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
methylFlow: cell-specific methylation pattern reconstruction from high-throughput bisulfite-converted DNA sequencing.
Dorri F, Mendelowitz L, Corrada Bravo H.
Bioinformatics. 2016 Jun 1;32(11):1618-24. doi: 10.1093/bioinformatics/btw287
:: DESCRIPTION
Phaser is a program for the rapid identification of linkage to recessive disease genes in either consanguineous or out-bred families, by reconstructing the haplotype for each individual’s chromosomes within a pedigree
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Carr IM, Diggle DP, Touqan N, Anwar R, Sheridan EG, Bonthron DT, Johnson CA, Ali M, Markham AF.
Identification of autosomal recessive disease loci using out-bred nuclear families.
Hum Mutat. 2012 Feb;33(2):338-42.
:: DESCRIPTION
ProCARs is a program used to reconstruct Ancestral gene orders as CARs (Contiguous Ancestral Regions) with a progressive homology-based method. The method runs from a phylogeny tree (without branch lengths needed) with a marked ancestor and a block file.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Perrin A, Varré JS, Blanquart S, Ouangraoua A.
ProCARs: Progressive Reconstruction of Ancestral Gene Orders.
BMC Genomics. 2015;16 Suppl 5(Suppl 5):S6. doi: 10.1186/1471-2164-16-S5-S6. Epub 2015 May 26. PMID: 26040958; PMCID: PMC4460626.
:: DESCRIPTION
SPRUCE is an algorithm that infers a multi-state perfect phylogeny describing the evolutionary history of the somatic mutations (SNVs and CNVs) of a tumor given multi-sample bulk sequencing data. Specifically, the input to SPRUCE are variant allele frequencies and copy-number mixing proportions for each SNV in each sample.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
El-Kebir M, Satas G, Oesper L, Raphael BJ.
Inferring the Mutational History of a Tumor Using Multi-state Perfect Phylogeny Mixtures.
Cell Syst. 2016 Jul;3(1):43-53. doi: 10.1016/j.cels.2016.07.004. PMID: 27467246.
:: DESCRIPTION
PREGO reconstructs a cancer genome as a rearrangement of segments, or intervals, from the reference genome using paired end sequencing data
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
L. Oesper, A. Ritz, S.J. Aerni, R. Drebin, and B.J. Raphael. (2012)
Reconstructing Cancer Genome Organization.
BMC Bioinformatics. 2012; 13(Suppl 6): S10.
:: DESCRIPTION
FEMER (FEtal MEthylome Reconstructor) is a novel size-based algorithm to noninvasively reconstruct the placental methylome by genomewide bisulfite sequencing and size-based analysis of maternal plasma DNA.
::DEVELOPER
Dr. Sun Hao’s Bioinformatics Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Sun K, Lun FMF, Leung TY, Chiu RWK, Lo YMD, Sun H.
Noninvasive reconstruction of placental methylome from maternal plasma DNA: Potential for prenatal testing and monitoring.
Prenat Diagn. 2018 Feb;38(3):196-203. doi: 10.1002/pd.5214. Epub 2018 Jan 31. PMID: 29334402.
