Molloy et al., 2019 - Google Patents
TreeMerge: a new method for improving the scalability of species tree estimation methodsMolloy et al., 2019
View HTML- Document ID
- 16922786272042339173
- Author
- Molloy E
- Warnow T
- Publication year
- Publication venue
- Bioinformatics
External Links
Snippet
Abstract Motivation At RECOMB-CG 2018, we presented NJMerge and showed that it could be used within a divide-and-conquer framework to scale computationally intensive methods for species tree estimation to larger datasets. However, NJMerge has two significant …
- 241000894007 species 0 title abstract description 109
Classifications
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
- G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
- G06F17/30286—Information retrieval; Database structures therefor; File system structures therefor in structured data stores
- G06F17/30312—Storage and indexing structures; Management thereof
- G06F17/30321—Indexing structures
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
- G06F19/22—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or SNP [Single-Nucleotide Polymorphism] discovery or sequence alignment
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
- G06F19/16—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for molecular structure, e.g. structure alignment, structural or functional relations, protein folding, domain topologies, drug targeting using structure data, involving two-dimensional or three-dimensional structures
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
- G06F19/28—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for programming tools or database systems, e.g. ontologies, heterogeneous data integration, data warehousing or computing architectures
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
- G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
- G06F17/30943—Information retrieval; Database structures therefor; File system structures therefor details of database functions independent of the retrieved data type
- G06F17/30946—Information retrieval; Database structures therefor; File system structures therefor details of database functions independent of the retrieved data type indexing structures
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
- G06F19/24—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for machine learning, data mining or biostatistics, e.g. pattern finding, knowledge discovery, rule extraction, correlation, clustering or classification
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
- G06F19/18—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
- G06F17/20—Handling natural language data
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06Q—DATA PROCESSING SYSTEMS OR METHODS, SPECIALLY ADAPTED FOR ADMINISTRATIVE, COMMERCIAL, FINANCIAL, MANAGERIAL, SUPERVISORY OR FORECASTING PURPOSES; SYSTEMS OR METHODS SPECIALLY ADAPTED FOR ADMINISTRATIVE, COMMERCIAL, FINANCIAL, MANAGERIAL, SUPERVISORY OR FORECASTING PURPOSES, NOT OTHERWISE PROVIDED FOR
- G06Q10/00—Administration; Management
- G06Q10/06—Resources, workflows, human or project management, e.g. organising, planning, scheduling or allocating time, human or machine resources; Enterprise planning; Organisational models
- G06Q10/063—Operations research or analysis
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F8/00—Arrangements for software engineering
- G06F8/70—Software maintenance or management
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/70—Chemoinformatics, i.e. data processing methods or systems for the retrieval, analysis, visualisation, or storage of physicochemical or structural data of chemical compounds
- G06F19/708—Chemoinformatics, i.e. data processing methods or systems for the retrieval, analysis, visualisation, or storage of physicochemical or structural data of chemical compounds for data visualisation, e.g. molecular structure representations, graphics generation, display of maps or networks or other visual representations
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F9/00—Arrangements for programme control, e.g. control unit
- G06F9/06—Arrangements for programme control, e.g. control unit using stored programme, i.e. using internal store of processing equipment to receive and retain programme
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06Q—DATA PROCESSING SYSTEMS OR METHODS, SPECIALLY ADAPTED FOR ADMINISTRATIVE, COMMERCIAL, FINANCIAL, MANAGERIAL, SUPERVISORY OR FORECASTING PURPOSES; SYSTEMS OR METHODS SPECIALLY ADAPTED FOR ADMINISTRATIVE, COMMERCIAL, FINANCIAL, MANAGERIAL, SUPERVISORY OR FORECASTING PURPOSES, NOT OTHERWISE PROVIDED FOR
- G06Q10/00—Administration; Management
- G06Q10/10—Office automation, e.g. computer aided management of electronic mail or groupware; Time management, e.g. calendars, reminders, meetings or time accounting
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F15/00—Digital computers in general; Data processing equipment in general
- G06F15/16—Combinations of two or more digital computers each having at least an arithmetic unit, a programme unit and a register, e.g. for a simultaneous processing of several programmes
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F11/00—Error detection; Error correction; Monitoring
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F21/00—Security arrangements for protecting computers, components thereof, programs or data against unauthorised activity
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06Q—DATA PROCESSING SYSTEMS OR METHODS, SPECIALLY ADAPTED FOR ADMINISTRATIVE, COMMERCIAL, FINANCIAL, MANAGERIAL, SUPERVISORY OR FORECASTING PURPOSES; SYSTEMS OR METHODS SPECIALLY ADAPTED FOR ADMINISTRATIVE, COMMERCIAL, FINANCIAL, MANAGERIAL, SUPERVISORY OR FORECASTING PURPOSES, NOT OTHERWISE PROVIDED FOR
- G06Q30/00—Commerce, e.g. shopping or e-commerce
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06Q—DATA PROCESSING SYSTEMS OR METHODS, SPECIALLY ADAPTED FOR ADMINISTRATIVE, COMMERCIAL, FINANCIAL, MANAGERIAL, SUPERVISORY OR FORECASTING PURPOSES; SYSTEMS OR METHODS SPECIALLY ADAPTED FOR ADMINISTRATIVE, COMMERCIAL, FINANCIAL, MANAGERIAL, SUPERVISORY OR FORECASTING PURPOSES, NOT OTHERWISE PROVIDED FOR
- G06Q50/00—Systems or methods specially adapted for a specific business sector, e.g. utilities or tourism
- G06Q50/01—Social networking
Similar Documents
| Publication | Publication Date | Title |
|---|---|---|
| Stamatakis et al. | Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data | |
| Molloy et al. | TreeMerge: a new method for improving the scalability of species tree estimation methods | |
| Wu et al. | Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees | |
| Löytynoja et al. | Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm | |
| Willson et al. | DISCO: species tree inference using multicopy gene family tree decomposition | |
| Pardi et al. | Reconstructible phylogenetic networks: do not distinguish the indistinguishable | |
| Depolli et al. | Exact parallel maximum clique algorithm for general and protein graphs | |
| Nelesen et al. | DACTAL: divide-and-conquer trees (almost) without alignments | |
| Geraci | A comparison of several algorithms for the single individual SNP haplotyping reconstruction problem | |
| Noutahi et al. | Efficient gene tree correction guided by genome evolution | |
| Vachaspati et al. | FastRFS: fast and accurate Robinson-Foulds Supertrees using constrained exact optimization | |
| Gao et al. | TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain | |
| Lin et al. | Kart: a divide-and-conquer algorithm for NGS read alignment | |
| Santana-Quintero et al. | HIVE-hexagon: high-performance, parallelized sequence alignment for next-generation sequencing data analysis | |
| Mirzaei et al. | RENT+: an improved method for inferring local genealogical trees from haplotypes with recombination | |
| Lutteropp et al. | NetRAX: accurate and fast maximum likelihood phylogenetic network inference | |
| Sahlin et al. | Assembly scaffolding with PE-contaminated mate-pair libraries | |
| Hossain et al. | Crystallizing short-read assemblies around seeds | |
| Vernygora et al. | Evaluating the performance of probabilistic algorithms for phylogenetic analysis of big morphological datasets: a simulation study | |
| Mazrouee et al. | FastHap: fast and accurate single individual haplotype reconstruction using fuzzy conflict graphs | |
| Dencker et al. | ‘Multi-SpaM’: a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees | |
| Molloy et al. | NJMerge: a generic technique for scaling phylogeny estimation methods and its application to species trees | |
| Domazet-Lošo et al. | Efficient estimation of pairwise distances between genomes | |
| Gunawan et al. | A program for verification of phylogenetic network models | |
| Valle et al. | Optimization strategies for fast detection of positive selection on phylogenetic trees |