
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 nonbinary 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 nonbinary. We present the first ... outputs a reconciliation of a nonbinary 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 treebuilding 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 highdensity genotype data ... eQTL mapping in homozygous inbred populations with binary allele calls. FastMap exploits the discrete nature ... organized into a Hamming distancebased 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, treebased association mapping methods show obvious advantages ... analysis. However, existing treebased 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 Booleantreebased 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 genegene and geneenvironment 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 659 articles
[sw00143]
 CoCoA is a system for Computations in Commutative...

Macaulay2
 Referenced in 1924 articles
[sw00537]
 Macaulay2 is a software system devoted to supporting...

Maple
 Referenced in 5375 articles
[sw00545]
 The result of over 30 years of cutting...

Mathematica
 Referenced in 6360 articles
[sw00554]
 Almost any workflow involves computing results, and that...

Matlab
 Referenced in 13559 articles
[sw00558]
 MATLAB® is a highlevel language and interactive...

nauty
 Referenced in 609 articles
[sw00611]
 graphtheoretic program NAUTY: nauty is a program...

NetworkX
 Referenced in 166 articles
[sw00616]
 NetworkX (NX) is a Python package for the...

QAPLIB
 Referenced in 233 articles
[sw00751]
 A collection of electronically available data instances for...

R
 Referenced in 10082 articles
[sw00771]
 R is a language and environment for statistical...

SageMath
 Referenced in 2021 articles
[sw00825]
 Sage (SageMath) is free, opensource math software...

SINGULAR
 Referenced in 1509 articles
[sw00866]
 SINGULAR is a Computer Algebra system (CAS) for...