• ecceTERA

  • Referenced in 6 articles [sw24891]
  • generic parsimony reconciliation algorithm, which accounts for gene duplication, loss and transfer (DTL) as well ... undated, fully dated or partially dated species trees. The ecceTERA reconciliation model and algorithm generalize ... algorithms for binary species trees and binary gene trees. Moreover, ecceTERA can estimate accurate species...
  • TxT

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

  • Referenced in 1 article [sw29603]
  • correct, a posteriori, errors in gene trees inferred from multiple sequence alignments. Unfortunately the best ... algorithm for reconstructing a binary gene tree with branch length. GATC returns optimal solutions according...
  • SuperTriplets

  • Referenced in 3 articles [sw29604]
  • Phylogenetic tree-building methods use molecular data to represent the evolutionary history of genes ... step approach whereby a binary representation of the initial trees is first inferred and then...
  • OCTAL

  • Referenced in 2 articles [sw29609]
  • completion of gene trees is desirable. Results: We introduce the Optimal Tree Completion problem ... problem that involves completing an unrooted binary tree (i.e., adding missing leaves ... minimize its distance from a reference tree on a superset of the leaves. We present ... this problem when the distance between trees is defined using the Robinson–Foulds (RF) distance...
  • FastMap

  • Referenced in 3 articles [sw20452]
  • regulate transcript expression. The availability of both gene expression and high-density genotype data ... eQTL mapping in homozygous inbred populations with binary allele calls. FastMap exploits the discrete nature ... organized into a Hamming distance-based tree that minimizes the number of arithmetic operations required...
  • TreeQA

  • Referenced in 1 article [sw20041]
  • mapping in modern genetics is to identify genes or narrow regions in the genome that ... morphology or disease. Among the existing methods, tree-based association mapping methods show obvious advantages ... analysis. However, existing tree-based methods are designed primarily for binary phenotypes derived from case/control...
  • Jimena

  • Referenced in 1 article [sw29354]
  • inputs. Many GRNs from literature or new gene expression experiments exceed those limitations ... framework Jimena we introduce and setup Boolean-tree-based data structures; (ii) corresponding algorithms greatly ... models are efficiently counted and identified using binary decision diagrams. As application example, we show...
  • OrdLogReg

  • Referenced in 1 article [sw26696]
  • diseases arise from complex gene-gene and gene-environment interactions, patient strata may be defined ... enables modeling a binary outcome using logical combinations of binary predictors yielding easily interpretable models ... simulations comparing OLR and Classification and Regression Trees (CART) demonstrate that OLR is superior...
  • CoCoA

  • Referenced in 637 articles [sw00143]
  • CoCoA is a system for Computations in Commutative...
  • Macaulay2

  • Referenced in 1734 articles [sw00537]
  • Macaulay2 is a software system devoted to supporting...
  • Maple

  • Referenced in 5177 articles [sw00545]
  • The result of over 30 years of cutting...
  • Mathematica

  • Referenced in 6075 articles [sw00554]
  • Almost any workflow involves computing results, and that...
  • Matlab

  • Referenced in 12557 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • nauty

  • Referenced in 575 articles [sw00611]
  • graph-theoretic program NAUTY: nauty is a program...
  • QAPLIB

  • Referenced in 222 articles [sw00751]
  • A collection of electronically available data instances for...
  • R

  • Referenced in 8776 articles [sw00771]
  • R is a language and environment for statistical...
  • SageMath

  • Referenced in 1741 articles [sw00825]
  • Sage (SageMath) is free, open-source math software...
  • SINGULAR

  • Referenced in 1424 articles [sw00866]
  • SINGULAR is a Computer Algebra system (CAS) for...
  • TSPLIB

  • Referenced in 674 articles [sw00983]
  • TSPLIB is a library of sample instances for...