Phangorn protocols

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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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Maintainer


  • person_outline Klaus Peter Schliep <>

Publication for Phangorn

Phangorn in pipelines

 (35)
2018
PMCID: 5810265
PMID: 29472894
DOI: 10.3389/fmicb.2017.02679

[…] as the number of times each branch in the original tree occurred in the set of bootstrap replicates (iq-tree option ‘-sup’)., the calculated phylogenetic tree was midpoint-rooted with the r package phangorn v2.0.4 (). for tree visualization itol v3.4.3 was used (). bootstrap values within a range of 95–100% were represented as filled circles of varying size. for better visualization […]

2018
PMCID: 5875798
PMID: 29596468
DOI: 10.1371/journal.pone.0194899

[…] based on a 325nt length amplicon, and for its was based on a variable length amplicon with a minimum of 50 nt length., the sequences were aligned with the ‘decipher’ package in r, output with the ‘phangorn’ package version 2.1.1 into fasttree 2 software for generation of a generalized time-reversible (gtr) maximum-likelihood phylogenetic tree with rescaling of branch lengths and computation […]

2018
PMCID: 5897096
PMID: 29648535
DOI: 10.7554/eLife.33034.033

[…] determined substitution model and rapid bootstrapping (1000 replications). the phylogenies were midpoint rooted and branches with local support less than 95 were collapsed using the ape and phangorn r packages (; ). phylogenies were visualized using itol version 3.0 ()., for the data included in , the number of genes for which a bacterial origin was confirmed after inspection […]

2018
PMCID: 5918592
PMID: 29292549
DOI: 10.1111/mec.14477

[…] (hd) was determined using the dnasp version 5 software (librado & rozas, ). a maximum‐likelihood tree was inferred with 1,000 bootstrap replicates and gaps treated as missing data using the phangorn packages in r (schliep, ), with the modeltest algorithm used to determine the best‐fit nucleotide substitution model, which was gtr+i+g (general time reversible model with a proportion […]

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

[…] matrix, where contrasts between treatments were examined through a test of homogeneity of dispersion (permdist in r), followed by tukeyhsd post-hoc tests., all trees for were built within the phangorn package through neighbor-joining, and annotation of trees was carried out in the figtree software (figtree 1.4.3 http://tree.bio.ed.ac.uk/software/figtree/)., the diatom cultures used […]


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Phangorn in publications

 (173)
PMCID: 5952469
PMID: 29764372
DOI: 10.1186/s12864-018-4751-5

[…] 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) […]

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

[…] 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 […]

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

[…] 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 […]

PMCID: 5928233
PMID: 29740479
DOI: 10.3389/fgene.2018.00147

[…] 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, )., in this study, we generated a resource dataset of 31,441,105 rainbow trout putative snps using whole genome shotgun resequencing for snp discovery in a panel of 11 dh lines […]

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 […]


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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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