DendroPy: a Python library for phylogenetic computing

By Jeet Sukumaran, Mark T. Holder. Bioinform., 2010

1,565 citations recorded by the source corpus.

Subfields: Ecological Modeling, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/cf9e352f57f0aba8fac2ba22929da397d4f09517

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Citations in the corpus

Molecular Evolution of Zika Virus during Its Emergence in the 20th Century (2014, neutral): “1 [47].”
ASTRAL: genome-scale coalescent-based species tree estimation (2014, methodology): “We evolved gene trees down the model tree under the multi-species coalescent model using Dendropy (Sukumaran and Holder, 2010), and then rescaled the gene trees to deviate from the molecular clock and produce branch length patterns observed in the biological data-set.”
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (2015, methodology): “12.0 (Sukumaran and Holder 2010) in order to root the trees between archaea and bacteria unless these groups were not monophyletic, in which case midpoint rooting was used.”
OpenStructure: an integrated software framework for computational structural biology (2013, background): “…there are many bioinformatics and structural biology toolkits that are either completely implemented in Python or provide a well maintained Python wrapper to their functionality (Sukumaran & Holder, 2010; Chaudhury et al., 2010; Hinsen & Sadron, 2000; Kohlbacher & Lenhof, 2000; Adams et al., 2011).”
Complex archaea that bridge the gap between prokaryotes and eukaryotes (2015, neutral): “MCG + C3 (0.03 / 0.24) Crenarchaeota (0 / 0) TA C K MHVG (0.03 / 0.19) Korarchaeota (0 / 0) Euryarchaeota (0 / 0) DPANN (2.1 / 15.7) 89 97 75 100 Loki’s Castle GC14 550 m 3,500 m K nipovich R idge Mo hn s R idg e Figure 1 | Identification of a novel archaeal lineage. a, Bathymetric map of the sampli”
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data (2016, background): “…and Bork 2007; Huson and Scornavacca 2012; Asnicar et al. 2015) and the programmatic manipulation of data (Paradis et al. 2004; Knight et al. 2007; Sukumaran and Holder 2010; Vos et al. 2011; Talevich et al. 2012), ETE offers a unified framework to compute and analyze genome-wide collections of…”
TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees (2018, positive): “com/uym2/ TreeShrink) using the Dendropy package [41].”
Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes (2015, methodology): “5 seconds per tree, and DendroPy [68] version 4.”
Elucidating modes of activation and herbicide resistance by sequence assembly and molecular modelling of the Acetolactate synthase complex in sugarcane. (2016, methodology): “Bootstrap replicates were mapped to the most likely tree using SumTrees (part of the DendroPy package) (Sukumaran and Holder, 2010).”
The fossilized birth–death process for coherent calibration of divergence-time estimates (2013, methodology): “Sukumaran J, Holder MT (2010) DendroPy: A Python library for phylogenetic computing.”
Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies (2015, methodology): “The bootstrap values were mapped to the species tree estimated from the original data matrix usingSumTrees v.3.3.1 (Sukumaran and Holder 2010).”
ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads (2017, methodology): “The distance between two samples is defined as the number of columns in the CSV file that agree, and an UPGMA tree is generated from the distance matrix using DendroPy [37].”