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Authors: Siavash Mirarab
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Journal Article

CONSULT-II: accurate taxonomic identification and profiling using locality-sensitive hashing

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Ali Osman Berk Şapcı and others
Bioinformatics, Volume 40, Issue 4, April 2024, btae150, https://doi.org/10.1093/bioinformatics/btae150
Published: 16 March 2024
Journal Article

Phylogenomic branch length estimation using quartets

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Yasamin Tabatabaee and others
Bioinformatics, Volume 39, Issue Supplement_1, June 2023, Pages i185–i193, https://doi.org/10.1093/bioinformatics/btad221
Published: 30 June 2023
Journal Article

Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using Mycobacterium tuberculosis isolates

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Afif Elghraoui and others
Bioinformatics, Volume 39, Issue 1, January 2023, btad024, https://doi.org/10.1093/bioinformatics/btad024
Published: 13 January 2023
Journal Article

ASTRAL-Pro 2: ultrafast species tree reconstruction from multi-copy gene family trees

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Chao Zhang and Siavash Mirarab
Bioinformatics, Volume 38, Issue 21, 1 November 2022, Pages 4949–4950, https://doi.org/10.1093/bioinformatics/btac620
Published: 12 September 2022
Journal Article

QuCo: quartet-based co-estimation of species trees and gene trees

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Maryam Rabiee and Siavash Mirarab
Bioinformatics, Volume 38, Issue Supplement_1, July 2022, Pages i413–i421, https://doi.org/10.1093/bioinformatics/btac265
Published: 27 June 2022
Journal Article

Completing gene trees without species trees in sub-quadratic time

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Uyen Mai and Siavash Mirarab
Bioinformatics, Volume 38, Issue 6, March 2022, Pages 1532–1541, https://doi.org/10.1093/bioinformatics/btab875
Published: 03 January 2022
Journal Article

SODA: multi-locus species delimitation using quartet frequencies

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Maryam Rabiee and Siavash Mirarab
Bioinformatics, Volume 36, Issue 24, December 2020, Pages 5623–5631, https://doi.org/10.1093/bioinformatics/btaa1010
Published: 08 February 2021
Journal Article

Phylogenetic double placement of mixed samples

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Metin Balaban and Siavash Mirarab
Bioinformatics, Volume 36, Issue Supplement_1, July 2020, Pages i335–i343, https://doi.org/10.1093/bioinformatics/btaa489
Published: 13 July 2020
Journal Article

TADA: phylogenetic augmentation of microbiome samples enhances phenotype classification

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Erfan Sayyari and others
Bioinformatics, Volume 35, Issue 14, July 2019, Pages i31–i40, https://doi.org/10.1093/bioinformatics/btz394
Published: 05 July 2019
Journal Article

ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization

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John Yin and others
Bioinformatics, Volume 35, Issue 20, October 2019, Pages 3961–3969, https://doi.org/10.1093/bioinformatics/btz211
Published: 23 March 2019
Journal Article

FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences

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Niema Moshiri and others
Bioinformatics, Volume 35, Issue 11, June 2019, Pages 1852–1861, https://doi.org/10.1093/bioinformatics/bty921
Published: 05 November 2018
Journal Article

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

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Siavash Mirarab and Tandy Warnow
Bioinformatics, Volume 31, Issue 12, June 2015, Pages i44–i52, https://doi.org/10.1093/bioinformatics/btv234
Published: 10 June 2015
Journal Article

TIPP: taxonomic identification and phylogenetic profiling

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Nam-phuong Nguyen and others
Bioinformatics, Volume 30, Issue 24, December 2014, Pages 3548–3555, https://doi.org/10.1093/bioinformatics/btu721
Published: 29 October 2014
Journal Article

FASTSP: linear time calculation of alignment accuracy

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Siavash Mirarab and Tandy Warnow
Bioinformatics, Volume 27, Issue 23, December 2011, Pages 3250–3258, https://doi.org/10.1093/bioinformatics/btr553
Published: 07 October 2011