An Opiliones-specific ultraconserved element probe set with a near-complete family-level phylogeny

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

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BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan, Ira M. Hall · Bioinformatics · 2010 · 30.4K citations · Full text

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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

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SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

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ModelFinder: fast model selection for accurate phylogenetic estimates

Subha Kalyaanamoorthy, Bùi Quang Minh, Thomas K. F. Wong et al. · Nature Methods · 2017 · 18.8K citations

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