DeCoSTAR - Detection of Co-evolution
DeCoSTAR is a software which aims at reconstructing ancestral gene or genome organizations, in the form of sets of neighborhood relations -adjacencies- between pairs of ancestral genes or gene domains.Ancestral genes or domains are deduced from reconciled gene trees in a context of birth, speciat...Tags: Bioinformatics, DeCoSTAR, Detection, Co-evolution, Reconstruction, Ancestral, Gene, Genome
2581 days ago
CAR: Reconstructing Contiguous Regions of an Ancestral Genome
We describe a new method for predicting the ancestral order and orientation of those intervals from their observed adjacencies in modern species. We combine the results from this method with data from chromosome painting experiments to produce a map of an early mammalian genome that accounts fo...Tags: Reconstruction, Contiguous, Regions, Ancestral, Genome, Bioinformatics, CAR
2547 days ago
ANGES: reconstructing ANcestral GEnomeS maps
This page contains the software ANGES 1.01, that aims at reconstucting ancestral genome maps from homologous markers in extant related genomes. Download Program, version 1.01 (July 10, 2012, documentation updated in August 2014) Examples with results (featured ancestors: boreoeutherian,...Tags: Reconstruction, Ancestral, Genomes, Maps, ANGES
2547 days ago
Tags: DESCHRAMBLER, Synteny, Ancestral, Reconstruction, Genome
2504 days ago
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single comm...Tags: ETE3, Reconstruction, Analysis, Visualization, Phylogenomic, Data
2270 days ago
REGEN: Ancestral Genome Reconstruction for Bacteria
REGEN infers evolutionary events, including gene creation and deletion and replicon fission and fusion. The reconstruction can be performed by either a maximum parsimony or a maximum likelihood method. Gene content reconstruction is based on the concept of neighboring gene pairs. REGEN was design...Tags: REGEN, Ancestral, Genome, Reconstruction, Bacteria
2255 days ago
Tags: RAVEN, Reconstruction, Analysis, Visualization, Metabolic, Networks, Toolbox, software, suite, Matlab, semi-automated, reconstruction, genome-scale, models, GEMs
2022 days ago
DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies
DeCoSTAR computes adjacency evolutionary scenarios using a scoring scheme based on a weighted sum of adjacency gains and breakages. Solutions, both optimal and near-optimal, are sampled according to the Boltzmann–Gibbs distribution centered around parsimonious solutions, and statistical sup...Tags: DeCoSTAR, Reconstruction, Ancestral, Organization, Genes, Genomes, Reconciled, Phylogenies
1586 days ago
AGORA: Algorithm for Gene Order Reconstruction in Ancestors
AGORA stands for “Algorithm for Gene Order Reconstruction in Ancestors” and was developed by Matthieu Muffato in the DYOGEN Laboratory at the École normale supérieure in Paris in 2008. // | | // ) ) // ) ) // ) ) // | | //__| | // // / ...Tags: AGORA, Algorithm, Gene, Order, Reconstruction, Ancestors
799 days ago
mixtureS: a novel tool for bacterial strain reconstruction from reads
mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, without prior knowledge about the strains and their variations. Tested on 243 simulated datasets and 195 experimental datasets, mixtureS reliably identified the strains, their numbers and ...Tags: mixtureS, novel, tool, bacterial, strain, reconstruction, reads
1356 days ago