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Protocols

Phangorn specifications

Information


Unique identifier OMICS_12497
Name Phangorn
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.4.0
Stability Stable
Requirements
methods, stats, parallel, graphics, Matrix, utils, testthat, Biostrings, grDevices, rmarkdown, knitr, xtable, quadprog, seqinr, R(≥3.2.0), magrittr, rgl, ape(≥5.0), igraph(≥1.0), fastmatch, Rcpp(≥0.12.0)
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Klaus Peter Schliep

Publication for Phangorn

Phangorn citations

 (237)
library_books

Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast

2018
BMC Genomics
PMCID: 5952469
PMID: 29764372
DOI: 10.1186/s12864-018-4751-5

[…] ribed above). The dissimilarity distance matrix was calculated by the R package poppr [] and used to construct the phylogenetic network with the Neighbor-Net algorithm as implemented in the R package phangorn [, ].Gene phylogenetic trees were constructed from predicted coding sequences of all here sequenced genomes and the reference genome. First, BLAST clustering (1e-40 e-value threshold) and ana […]

library_books

Acquisition and dissemination of cephalosporin resistant E. coli in migratory birds sampled at an Alaska landfill as inferred through genomic analysis

2018
Sci Rep
PMCID: 5943298
PMID: 29743625
DOI: 10.1038/s41598-018-25474-w

[…] ndel were considered a unique allele. Maximum likelihood phylogenetic trees of AMR genes with more than two alleles were estimated in the statistical programming language R (v3.3.3) using the package phangorn (v2.2.0). Separate nucleotide substitution model tests were performed on each gene alignment and the model with the lowest Akaike information criterion value was used to estimate phylogenies […]

library_books

Environmental fluctuations accelerate molecular evolution of thermal tolerance in a marine diatom

2018
Nat Commun
PMCID: 5928086
PMID: 29712900
DOI: 10.1038/s41467-018-03906-5

[…] e downstream statistical analyses implemented in R using the packages vegan (2.4–3), mixOmics (6.1–3), ade4 (1.7–10), topGO (2.26–0, with Bioconductor 3.4), biomaRt (2.3–0 with Bioconductor 3.4), and phangorn (2.2–0).The matrices were first used for PCAs based on Euclidean distance matrices. From these, we pulled the top 100 loadings for the two major axes of variation, and associated them to a tr […]

library_books

A New Single Nucleotide Polymorphism Database for Rainbow Trout Generated Through Whole Genome Resequencing

2018
Front Genet
PMCID: 5928233
PMID: 29740479
DOI: 10.3389/fgene.2018.00147

[…] elihood method from the DNAML program in the PHYLIP package (Felsenstein, ) and the number at each node represents the percentage bootstrap value determined with 1,000 re-samples using the R package “phangorn” (Schliep, ). […]

call_split

Do we treat our patients or rather periodontal microbes with adjunctive antibiotics in periodontal therapy? A 16S rDNA microbial community analysis

2018
PLoS One
PMCID: 5906003
PMID: 29668720
DOI: 10.1371/journal.pone.0195534
call_split See protocol

[…] that did not reach a plateau phase were rejected.After multiple alignment of RSVs with the command decipher::AlignSeqs from the R-package DECIPHER [] a neighbor-joining tree [] was created using the phangorn package []. Utilizing the R-package phyloseq v.1.19.1 [] the following sample specific details were combined: I) all non-chimeric RSVs along with their classification down to genus-level and […]

library_books

Transposable Element Genomic Fissuring in Pyrenophora teres Is Associated With Genome Expansion and Dynamics of Host–Pathogen Genetic Interactions

2018
Front Genet
PMCID: 5915480
PMID: 29720997
DOI: 10.3389/fgene.2018.00130

[…] constructed to inform the whole genome alignment. MinHash distance estimation between each unmasked genome was calculated using MASH () and distances converted to a tree using the R-language package phangorn (). Softmasked genomes were aligned using progressiveCactus (; ) to generate a hierarchical alignment (HAL) file. Genes were predicted from the multi-genome HAL dataset using Augustus-CGP (co […]

Citations

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Phangorn institution(s)
UMR CNRS 7138 Systématique, Adaptation, Evolution, Université Pierre et Marie Curie, Muséum National d'Histoire Naturelle, Paris, France
Phangorn funding source(s)
Muséum National D'Histoire Naturelle, Paris, France

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