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Protocols

DendroPy specifications

Information


Unique identifier OMICS_08877
Name DendroPy
Software type Framework/Library
Interface Command line interface
Restrictions to use License purchase required
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Version 4.2.0
Stability Stable
Requirements
DendroPy legacy
Maintained Yes

Subtool


  • SumTrees

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline Jeet Sukumaran

Publication for DendroPy

DendroPy citations

 (177)
library_books

Multiple origins of green blood in New Guinea lizards

2018
Sci Adv
PMCID: 5955620
PMID: 29774232
DOI: 10.1126/sciadv.aao5017

[…] ng trees as input and has been shown to be robust to effects of both incorrectly estimated gene trees and gene tree heterogeneity (). Extended majority-rule consensus (MRE) trees were estimated using sumtrees in DendroPy v3.2 (). After visually confirming species monophyly and topological concordance among data sets, we elected to proceed with the ONE and TWO data sets for all subsequent analyses […]

call_split

Structural patterns of selection and diversity for Plasmodium vivax antigens DBP and AMA1

2018
Malar J
PMCID: 5930944
PMID: 29720179
DOI: 10.1186/s12936-018-2324-3
call_split See protocol

[…] The DendroPy Python library [] was used to calculate Tajima’s D, Watterson’s Theta, mean pairwise differences and nucleotide diversity. Haplotype diversity was calculated using:H=nn-11-∑ixi2where xi is th […]

library_books

Sharing of photobionts in sympatric populations of Thamnolia and Cetraria lichens: evidence from high throughput sequencing

2018
Sci Rep
PMCID: 5849601
PMID: 29535321
DOI: 10.1038/s41598-018-22470-y

[…] model for sequence evolution using the jModelTest. The 1000 trees with the best likelihood score were compiled in one phylogeny that represents the 50% majority-rule consensus tree using the program SumTrees.Thamnolia and Cetraria are highly divergent mycobiont genera from Lecanoromycetes. Therefore we performed a separate phylogeny for samples of each genus based on the mycobiont Sanger sequence […]

library_books

Multiple origins of downy mildews and mito nuclear discordance within the paraphyletic genus Phytophthora

2018
PLoS One
PMCID: 5846723
PMID: 29529094
DOI: 10.1371/journal.pone.0192502

[…] um likelihood (ML) tree was inferred using the PartitionFinder scheme () employing 200 best-tree searches in the program Garli 2.01 [], with 1000 bootstrap replications providing support, added using Sumtrees.py []. A Bayesian likelihood consensus tree was inferred with MrBayes 3.2.6 [], using the closest approximation of the best PartitionFinder scheme and running generations until the standard d […]

library_books

Proteome wide mapping of immune features onto Plasmodium protein three dimensional structures

2018
Sci Rep
PMCID: 5847524
PMID: 29531293
DOI: 10.1038/s41598-018-22592-3

[…] ther a predefined or user-defined function, either with or without some level of spatial averaging. The package makes use of the BioPython Bio.PDB module for PDB file parsing and manipulation and the DendroPy package for calculation of Tajima’s D. The source code is available at https://github.com/andrewguy/biostructmap. For all structural mapping work using BioStructMap, protein chains were treat […]

library_books

The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence based framework for family level virus classification

2018
Microbiome
PMCID: 5819261
PMID: 29458427
DOI: 10.1186/s40168-018-0422-7

[…] dendrogram sample. The process was repeated 100 times to obtain a distribution of bootstrap dendrograms. We then computed bootstrap support for branches on the best-estimate UPGMA dendrogram by using SumTrees [] based on the obtained dendrogram distribution.It is possible that several low bootstrapped support values might be caused by empty profile sampling—i.e. all elements in the bootstrapped si […]

Citations

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DendroPy institution(s)
Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
DendroPy funding source(s)
Portions of DendroPy were developed under CIPRES, a multi-site collaboration funded by the NSF Information Technology Research (ITR) program grant entitled “BUILDING THE TREE OF LIFE: A National Resource for Phyloinformatics and Computational Phylogenetics” and NSF ATOL grant 0732920.

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