Results for "reconstruction"

Tags

  • 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

    2531 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

    2497 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

    2497 days ago

  • DESCHRAMBLER

    DESCHRAMBLER is shown to produce highly accurate reconstructions using data simulation and by benchmarking it against other reconstruction tools You can find the detail of reconstructed data at http://bioinfo.konkuk.ac.kr/DESCHRAMBLER/

    Tags: DESCHRAMBLER, Synteny, Ancestral, Reconstruction, Genome

    2455 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

    2220 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

    2205 days ago

  • RAVEN: a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models

    The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc databases, coupled with extensive gap-filling an...

    Tags: RAVEN, Reconstruction, Analysis, Visualization, Metabolic, Networks, Toolbox, software, suite, Matlab, semi-automated, reconstruction, genome-scale, models, GEMs

    1972 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

    1537 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

    749 days ago

  • Ancestral sequence reconstruction (ASR) or ancestral gene/sequence reconstruction/resurrection tools to study molecular evolution

    Ancestral sequence reconstruction (ASR) – also known as ancestral gene/sequence reconstruction/resurrection – is a technique used in the study of molecular evolution. The method consists of the synthesis of an ancestral gene and expression of the correspo...

    Tags: Ancestral, sequence, reconstruction, ASR, ancestral, gene, sequence, reconstruction, resurrection, technique, molecular, evolution

    2483 days ago