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sequence alignment (6) 6
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base sequence (5) 5
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[sdv.bid.evo]life sciences [q-bio]/biodiversity/populations and evolution [q-bio.pe] (3) 3
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1. Full Text ASTRAL-II: Coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
by Mirarab, Siavash and Warnow, Tandy
Bioinformatics, ISSN 1367-4803, 06/2015, Volume 31, Issue 12, pp. i44 - i52
Statistics & Probability | Biochemistry & Molecular Biology | Physical Sciences | Computer Science, Interdisciplinary Applications | Life Sciences & Biomedicine | Technology | Biochemical Research Methods | Computer Science | Mathematics | Biotechnology & Applied Microbiology | Science & Technology | Mathematical & Computational Biology | Data Interpretation, Statistical | Algorithms | Plants - genetics | Genes, Plant | Computer Simulation | Genetic Speciation | Genomics | Phylogeny | Plants - classification | Index Medicus | Ismb | Eccb 2015 Proceedings Papers Committee July 10 to July 14, 2015, Dublin, Ireland
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2. Full Text Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies
by Sayyari, Erfan and Mirarab, Siavash
Molecular biology and evolution, ISSN 0737-4038, 07/2016, Volume 33, Issue 7, pp. 1654 - 1668
branch length estimation | local support | quartet-based methods | multi-species coalescent | posterior probability | Incomplete lineage sorting | ASTRAL | Biochemistry & Molecular Biology | Genetics & Heredity | Life Sciences & Biomedicine | Evolutionary Biology | Science & Technology | Computational Biology - methods | Algorithms | Computer Simulation | Genetic Speciation | Bayes Theorem | Probability | Models, Genetic | Phylogeny | Genomics - methods | Index Medicus | Fast Track
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3. Full Text ASTRAL-III: Polynomial time species tree reconstruction from partially resolved gene trees
by Zhang, Chao and Rabiee, Maryam and Sayyari, Erfan and Mirarab, Siavash
BMC bioinformatics, ISSN 1471-2105, 05/2018, Volume 19, Issue Suppl 6, pp. 153 - 153
Incomplete lineage sorting | ASTRAL | Phylogenomics | Algorithms | Animals | Species Specificity | Time Factors | Computer Simulation | Databases, Genetic | Birds - classification | Models, Genetic | Phylogeny | Birds - genetics | Index Medicus
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4. Full Text Phylogenetic double placement of mixed samples
by Balaban, Metin and Mirarab, Siavash
Bioinformatics, ISSN 1367-4803, 07/2020, Volume 36, Issue Supplement_1, pp. i335 - i343
Index Medicus | Population Genomics and Molecular Evolution
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5. Full Text Log Transformation Improves Dating of Phylogenies
by Mai, Uyen and Mirarab, Siavash
Molecular biology and evolution, ISSN 0737-4038, 09/2020
Index Medicus
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6. Full Text Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting
by Siavash Mirarab and Md Shamsuzzoha Bayzid and Tandy Warnow
Systematic biology, ISSN 1063-5157, 5/2016, Volume 65, Issue 3, pp. 366 - 380
Datasets | Simulations | Maximum likelihood estimation | Taxa | Symposium | Genes | Phylogenetics | Turtles | Topology | Phylogeny | Estimation methods | Life Sciences & Biomedicine | Evolutionary Biology | Science & Technology | Gene Duplication | Probability | Classification - methods | Computer Simulation | Genetics | Accuracy | Genealogy | Estimating techniques | Maximum likelihood method | Index Medicus
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7. Full Text INSTRAL: Discordance-Aware Phylogenetic Placement Using Quartet Scores
by Rabiee, Maryam and Mirarab, Siavash
Systematic biology, ISSN 1063-5157, 03/2020, Volume 69, Issue 2, pp. 384 - 391
Life Sciences & Biomedicine | Evolutionary Biology | Science & Technology | Classification - methods | Software | Phylogeny | Sequence Analysis, DNA - methods | Index Medicus
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8. Full Text TreeShrink: Fast and accurate detection of outlier long branches in collections of phylogenetic trees
by Mai, Uyen and Mirarab, Siavash
BMC genomics, ISSN 1471-2164, 05/2018, Volume 19, Issue Suppl 5, pp. 272 - 272
Gene tree discordance | Rogue taxon removal | Tree diameter | Mammals - genetics | Computational Biology - methods | Mammals - classification | Datasets as Topic | Species Specificity | Genes | Humans | Phylogeny | Plants - classification | Algorithms | Animals | Plants - genetics | Models, Genetic | Software | Phylogenetic trees | Research | Analysis | Index Medicus
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9. Full Text A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition
by Moshiri, Niema and Mirarab, Siavash
Systematic biology, ISSN 1063-5157, 05/2018, Volume 67, Issue 3, pp. 475 - 489
Model | Evolution | Alu | Retrotransposition | Life Sciences & Biomedicine | Evolutionary Biology | Science & Technology | Models, Biological | Humans | Classification - methods | Phylogeny | Alu Elements - genetics | Genome, Human - genetics | Evolution, Molecular | Index Medicus | model | evolution | Regular | retrotransposition
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10. Full Text Forcing external constraints on tree inference using ASTRAL
by Rabiee, Maryam and Mirarab, Siavash
BMC genomics, ISSN 1471-2164, 04/2020, Volume 21, Issue Suppl 2, pp. 218 - 218
Trees | Computer simulation | Heuristic methods | Discordance | Genomes | Phylogeny | Optimization | Algorithms | Constraints | Phylogenetics | Dynamic programming | Species | Heuristic | Index Medicus | Tree completion | Constrained tree search | RF distance | ASTRAL
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11. Full Text Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction
by Sayyari, Erfan and Mirarab, Siavash
BMC genomics, ISSN 1471-2164, 11/2016, Volume 17, Issue Suppl 10, pp. 783 - 783
Quartet methods | Species tree | Multi-species coalescent | Incomplete lineage sorting | Genetic research | Origin of species | Genetic aspects | Phylogeny | Analysis | Index Medicus
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12. Full Text Phylogenomics: Constrained gene tree inference
by Mirarab, Siavash
Nature ecology & evolution, ISSN 2397-334X, 01/2017, Volume 1, Issue 2, pp. 56 - 56
Genes | Genomes | Phylogeny
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13. Full Text APPLES: Scalable Distance-Based Phylogenetic Placement with or without Alignments
by Balaban, Metin and Sarmashghi, Shahab and Mirarab, Siavash
Systematic biology, ISSN 1063-5157, 05/2020, Volume 69, Issue 3, pp. 566 - 578
Life Sciences & Biomedicine | Evolutionary Biology | Science & Technology | Classification - methods | Software | Algorithms | Phylogeny | Base Sequence | Index Medicus
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14. Full Text Statistical binning enables an accurate coalescent-based estimation of the avian tree
by Siavash Mirarab and Md. Shamsuzzoha Bayzid and Bastien Boussau and Tandy Warnow
Science (American Association for the Advancement of Science), ISSN 0036-8075, 12/2014, Volume 346, Issue 6215, pp. 1337 - 1337
RESEARCH ARTICLE SUMMARY | Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Mammals - genetics | Mammals - classification | Vertebrates - genetics | Computational Biology | Birds - classification | Phylogeny | Yeasts - genetics | Likelihood Functions | Sequence Alignment | Animals | Vertebrates - classification | Birds - genetics | Genome | Phylogenetics | Birds | Statistical analysis | Decision trees | Index Medicus | Trees | Production methods | Pipelines | Genes | Error detection | Graph theory | Estimates | Optimization
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