Cargando…

FASTRAL: improving scalability of phylogenomic analysis

MOTIVATION: ASTRAL is the current leading method for species tree estimation from phylogenomic datasets (i.e. hundreds to thousands of genes) that addresses gene tree discord resulting from incomplete lineage sorting (ILS). ASTRAL is statistically consistent under the multi-locus coalescent model (M...

Descripción completa

Detalles Bibliográficos
Autores principales:	Dibaeinia, Payam, Tabe-Bordbar, Shayan, Warnow, Tandy
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2021
Materias:	Original Papers
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8388037/ https://www.ncbi.nlm.nih.gov/pubmed/33576396 http://dx.doi.org/10.1093/bioinformatics/btab093

Ejemplares similares

Correction to: FASTRAL: improving scalability of phylogenomic analysis
Publicado: (2023)

SCAMPP+FastTree: improving scalability for likelihood-based phylogenetic placement
por: Chu, Gillian, et al.
Publicado: (2023)

Disk covering methods improve phylogenomic analyses
por: Bayzid, Md Shamsuzzoha, et al.
Publicado: (2014)

Fast and accurate methods for phylogenomic analyses
por: Yang, Jimmy, et al.
Publicado: (2011)

BBCA: Improving the scalability of *BEAST using random binning
por: Zimmermann, Théo, et al.
Publicado: (2014)

TreeMerge: a new method for improving the scalability of species tree estimation methods
por: Molloy, Erin K, et al.
Publicado: (2019)

Phylogenomic branch length estimation using quartets
por: Tabatabaee, Yasamin, et al.
Publicado: (2023)

Constrained incremental tree building: new absolute fast converging phylogeny estimation methods with improved scalability and accuracy
por: Zhang, Qiuyi, et al.
Publicado: (2019)

Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer
por: Davidson, Ruth, et al.
Publicado: (2015)

MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences
por: Shen, Chengze, et al.
Publicado: (2021)

Computational Analysis of the Hypothalamic Control of Food Intake
por: Tabe-Bordbar, Shayan, et al.
Publicado: (2016)

MAGUS: Multiple sequence Alignment using Graph clUStering
por: Smirnov, Vladimir, et al.
Publicado: (2020)

HMMerge: an ensemble method for multiple sequence alignment
por: Park, Minhyuk, et al.
Publicado: (2023)

WITCH-NG: efficient and accurate alignment of datasets with sequence length heterogeneity
por: Liu, Baqiao, et al.
Publicado: (2023)

Integrative modeling of lncRNA-chromatin interaction maps reveals diverse mechanisms of nuclear retention
por: Tabe-Bordbar, Shayan, et al.
Publicado: (2023)

Unblended disjoint tree merging using GTM improves species tree estimation
por: Smirnov, Vladimir, et al.
Publicado: (2020)

DISCO+QR: rooting species trees in the presence of GDL and ILS
por: Willson, James, et al.
Publicado: (2023)

Phylogenomic analyses data of the avian phylogenomics project
por: Jarvis, Erich D, et al.
Publicado: (2015)

Deciphering enhancer sequence using thermodynamics-based models and convolutional neural networks
por: Dibaeinia, Payam, et al.
Publicado: (2021)

TIPP2: metagenomic taxonomic profiling using phylogenetic markers
por: Shah, Nidhi, et al.
Publicado: (2021)

Standard maximum likelihood analyses of alignments with gaps can be statistically inconsistent
por: Warnow, Tandy
Publicado: (2012)

Concatenation Analyses in the Presence of Incomplete Lineage Sorting
por: Warnow, Tandy
Publicado: (2015)

Bioinformatics and phylogenetics: seminal contributions of Bernard Moret
por: Warnow, Tandy
Publicado: (2019)

UPP2: fast and accurate alignment of datasets with fragmentary sequences
por: Park, Minhyuk, et al.
Publicado: (2023)

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
por: Mirarab, Siavash, et al.
Publicado: (2015)

A closer look at cross-validation for assessing the accuracy of gene regulatory networks and models
por: Tabe-Bordbar, Shayan, et al.
Publicado: (2018)

Treelength Optimization for Phylogeny Estimation
por: Liu, Kevin, et al.
Publicado: (2012)

ASTRID: Accurate Species TRees from Internode Distances
por: Vachaspati, Pranjal, et al.
Publicado: (2015)

Scaling statistical multiple sequence alignment to large datasets
por: Nute, Michael, et al.
Publicado: (2016)

FastRFS: fast and accurate Robinson-Foulds Supertrees using constrained exact optimization
por: Vachaspati, Pranjal, et al.
Publicado: (2017)

SIESTA: enhancing searches for optimal supertrees and species trees
por: Vachaspati, Pranjal, et al.
Publicado: (2018)

PASTA for proteins
por: Collins, Kodi, et al.
Publicado: (2018)

Phylogeny Estimation Given Sequence Length Heterogeneity
por: Smirnov, Vladimir, et al.
Publicado: (2020)

Recent progress on methods for estimating and updating large phylogenies
por: Zaharias, Paul, et al.
Publicado: (2022)

Weighted ASTRID: fast and accurate species trees from weighted internode distances
por: Liu, Baqiao, et al.
Publicado: (2023)

EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure
por: Dieckmann, Marius Alfred, et al.
Publicado: (2021)

Gene tree parsimony for incomplete gene trees: addressing true biological loss
por: Bayzid, Md Shamsuzzoha, et al.
Publicado: (2018)

Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge
por: Molloy, Erin K., et al.
Publicado: (2019)

FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models
por: Molloy, Erin K, et al.
Publicado: (2020)

Sifter-T: A scalable framework for phylogenomic probabilistic protein domain functional annotation
por: Almeida-E-Silva, Danillo C, et al.
Publicado: (2015)

Cannot write session to /tmp/vufind_sessions/sess_15ciuhtmjae25ngfeq11l0q94r