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Journal Article

PhyloAln: A Convenient Reference-Based Tool to Align Sequences and High-Throughput Reads for Phylogeny and Evolution in the Omic Era

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Yu-Hao Huang and others
Molecular Biology and Evolution, Volume 41, Issue 7, July 2024, msae150, https://doi.org/10.1093/molbev/msae150
Published: 23 July 2024
Journal Article

phyloBARCODER: A Web Tool for Phylogenetic Classification of Eukaryote Metabarcodes Using Custom Reference Databases

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Jun Inoue and others
Molecular Biology and Evolution, Volume 41, Issue 8, August 2024, msae111, https://doi.org/10.1093/molbev/msae111
Published: 08 June 2024
Journal Article

PhyloBench: A Benchmark for Evaluating Phylogenetic Programs

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Sergey Spirin and others
Molecular Biology and Evolution, Volume 41, Issue 6, June 2024, msae084, https://doi.org/10.1093/molbev/msae084
Published: 11 May 2024
Journal Article

scalepopgen: Bioinformatic Workflow Resources Implemented in Nextflow for Comprehensive Population Genomic Analyses

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Maulik Upadhyay and others
Molecular Biology and Evolution, Volume 41, Issue 4, April 2024, msae057, https://doi.org/10.1093/molbev/msae057
Published: 20 March 2024
Journal Article

PAPipe: A Pipeline for Comprehensive Population Genetic Analysis

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Nayoung Park and others
Molecular Biology and Evolution, Volume 41, Issue 3, March 2024, msae040, https://doi.org/10.1093/molbev/msae040
Published: 01 March 2024
Journal Article

PlantFUNCO: Integrative Functional Genomics Database Reveals Clues into Duplicates Divergence Evolution

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Víctor Roces and others
Molecular Biology and Evolution, Volume 41, Issue 3, March 2024, msae042, https://doi.org/10.1093/molbev/msae042
Published: 27 February 2024
Journal Article

Ursa: A Comprehensive Multiomics Toolbox for High-Throughput Single-Cell Analysis

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Lu Pan and others
Molecular Biology and Evolution, Volume 40, Issue 12, December 2023, msad267, https://doi.org/10.1093/molbev/msad267
Published: 13 December 2023
Journal Article

A Fast, Reproducible, High-throughput Variant Calling Workflow for Population Genomics

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Cade D Mirchandani and others
Molecular Biology and Evolution, Volume 41, Issue 1, January 2024, msad270, https://doi.org/10.1093/molbev/msad270
Published: 09 December 2023
Journal Article

IPOP: An Integrative Plant Multi-omics Platform for Cross-species Comparison and Evolutionary Study

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Wenyue Huang and others
Molecular Biology and Evolution, Volume 40, Issue 12, December 2023, msad248, https://doi.org/10.1093/molbev/msad248
Published: 23 November 2023
Journal Article

MitoFish, MitoAnnotator, and MiFish Pipeline: Updates in 10 Years

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Tao Zhu and others
Molecular Biology and Evolution, Volume 40, Issue 3, March 2023, msad035, https://doi.org/10.1093/molbev/msad035
Published: 28 February 2023
Journal Article

A Phylogenetic Framework to Simulate Synthetic Interspecies RNA-Seq Data

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Paul Bastide and others
Molecular Biology and Evolution, Volume 40, Issue 1, January 2023, msac269, https://doi.org/10.1093/molbev/msac269
Published: 12 December 2022
Journal Article

tidy tree: A New Layout for Phylogenetic Trees

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Simon Penel and Damien M de Vienne
Molecular Biology and Evolution, Volume 39, Issue 10, October 2022, msac204, https://doi.org/10.1093/molbev/msac204
Published: 26 September 2022
Journal Article

TimeTree 5: An Expanded Resource for Species Divergence Times

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Sudhir Kumar and others
Molecular Biology and Evolution, Volume 39, Issue 8, August 2022, msac174, https://doi.org/10.1093/molbev/msac174
Published: 06 August 2022
Journal Article

HAlign 3: Fast Multiple Alignment of Ultra-Large Numbers of Similar DNA/RNA Sequences

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Furong Tang and others
Molecular Biology and Evolution, Volume 39, Issue 8, August 2022, msac166, https://doi.org/10.1093/molbev/msac166
Published: 02 August 2022
Journal Article

The Codon Statistics Database: A Database of Codon Usage Bias

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Krishnamurthy Subramanian and others
Molecular Biology and Evolution, Volume 39, Issue 8, August 2022, msac157, https://doi.org/10.1093/molbev/msac157
Published: 21 July 2022
Journal Article

Tree House Explorer: A Novel Genome Browser for Phylogenomics

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Andrew J Harris and others
Molecular Biology and Evolution, Volume 39, Issue 6, June 2022, msac130, https://doi.org/10.1093/molbev/msac130
Published: 14 June 2022
Journal Article

Real-Time and Remote MCMC Trace Inspection with Beastiary

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Wytamma Wirth and Sebastian Duchene
Molecular Biology and Evolution, Volume 39, Issue 5, May 2022, msac095, https://doi.org/10.1093/molbev/msac095
Published: 12 May 2022
Journal Article

AliSim: A Fast and Versatile Phylogenetic Sequence Simulator for the Genomic Era

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Nhan Ly-Trong and others
Molecular Biology and Evolution, Volume 39, Issue 5, May 2022, msac092, https://doi.org/10.1093/molbev/msac092
Published: 03 May 2022
Journal Article

FishmiRNA: An Evolutionarily Supported MicroRNA Annotation and Expression Database for Ray-Finned Fishes

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Thomas Desvignes and others
Molecular Biology and Evolution, Volume 39, Issue 2, February 2022, msac004, https://doi.org/10.1093/molbev/msac004
Published: 10 January 2022
Journal Article

ORTHOSCOPE*: A Phylogenetic Pipeline to Infer Gene Histories from Genome-Wide Data

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Jun Inoue
Molecular Biology and Evolution, Volume 39, Issue 1, January 2022, msab301, https://doi.org/10.1093/molbev/msab301
Published: 18 October 2021