• GloMIQO

  • Referenced in 82 articles [sw06266]
  • reactor-separator-recycle systems, separation systems, data reconciliation, batch processes, crude oil scheduling, and natural...
  • par2Dhp

  • Referenced in 17 articles [sw30807]
  • algorithms for parallel mesh refinement and mesh reconciliation. The application was written in Fortran...
  • Isabelle/UTP

  • Referenced in 14 articles [sw21184]
  • Additionally, our work provides novel insights towards reconciliation of shallow and deep language embeddings...
  • ecceTERA

  • Referenced in 6 articles [sw24891]
  • ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony. A gene tree-species tree reconciliation ... program that implements a generic parsimony reconciliation algorithm, which accounts for gene duplication, loss ... partially dated species trees. The ecceTERA reconciliation model and algorithm generalize or improve upon most...
  • SLPTESTSET

  • Referenced in 10 articles [sw07565]
  • short description, mathematical problem statement, and notational reconciliation to a standard problem format. In addition...
  • iGTP

  • Referenced in 5 articles [sw23050]
  • duplication, duplication-loss, and deep coalescence reconciliation costs. iGTP significantly extends and improves the functionality ... duplication, duplication-loss, and deep coalescence reconciliation costs, all from within a convenient graphical user...
  • BUCKy

  • Referenced in 7 articles [sw23619]
  • BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis. Motivation: BUCKy is a C++ program...
  • Unison

  • Referenced in 4 articles [sw13307]
  • replicated directory structures. Like other replication and reconciliation facilities provided by modern operating systems ... into account the possibility of failures during reconciliation, then refine it again to cover synchronization...
  • hts

  • Referenced in 4 articles [sw31355]
  • include bottom-up, top-down, optimal combination reconciliation (Hyndman et al. 2011) reconciliation (Wickramasuriya et al. 2018)
  • DupTree

  • Referenced in 5 articles [sw12376]
  • examine alternate rootings and to weight the reconciliation costs for gene trees. DupTree...
  • SimPhy

  • Referenced in 5 articles [sw17058]
  • duplication time when using standard reconciliation methods. SimPhy is available at https://github.com/adamallo/SimPhy, where...
  • APMonitor

  • Referenced in 5 articles [sw19694]
  • MILP, MINLP). Modes of operation include data reconciliation, real-time optimization, dynamic simulation, and nonlinear...
  • SylvX

  • Referenced in 2 articles [sw34226]
  • SylvX: a viewer for phylogenetic tree reconciliations. Reconciliation methods aim at recovering the evolutionary processes ... interpret, and despite the fact that reconciliations are increasingly used, there is a shortage ... graphical management. Here we present SylvX, a reconciliation viewer which implements classical phylogenetic graphic operators ... methods to ease interpretation and comparison of reconciliations (multiple maps, moving, shrinking sub-reconciliations...
  • TERA

  • Referenced in 4 articles [sw34318]
  • Here, we present the Tree Estimation using Reconciliation (TERA) algorithm, a parsimony based, species tree...
  • MURPAR

  • Referenced in 2 articles [sw29666]
  • collection of gene trees by using pairwise reconciliations of trees in the collection. Given ... accurate methods for pairwise gene tree reconciliations, MURPAR inherits this efficiency and accuracy. Further ... method includes a formulation for combining pairwise reconciliations that is naturally amenable to an efficient...
  • RANGER-DTL

  • Referenced in 1 article [sw34144]
  • gene family evolution using Duplication-Transfer-Loss reconciliation. This new software is highly scalable ... features not currently available in any other reconciliation program. RANGER-DTL 2.0 has a particular ... focus on reconciliation accuracy and can account for many sources of reconciliation uncertainty including uncertain ... rooting, gene tree topological uncertainty, multiple optimal reconciliations and alternative event cost assignments. RANGER...
  • TxT

  • Referenced in 1 article [sw07679]
  • linear-time algorithm for reconciliation of non-binary gene tree and binary species tree Tree ... reconciliation approach to inferring the duplication history for a gene family poses challenging problems when ... first linear-time algorithm that outputs a reconciliation of a non-binary gene tree...
  • GATC

  • Referenced in 1 article [sw29603]
  • gene trees. Some of them use reconciliation with a species tree to correct, a posteriori ... likelihood (according to sequence evolution) and a reconciliation score under the Duplication-Transfer-Loss...
  • Ontograte

  • Referenced in 1 article [sw00651]
  • automatic ontology mapping system which leverages object reconciliation and multi-relational data mining techniques...
  • DDASAC

  • Referenced in 1 article [sw33454]
  • attraction of a solution. Options include automatic reconciliation of inconsistent initial states and derivatives, automatic...