Notung protocols

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Notung specifications

Information


Unique identifier OMICS_08809
Name Notung
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.6
Stability Stable
Maintained Yes

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Publication for Notung

Notung in pipelines

 (9)
2015
PMCID: 4351887
PMID: 25748510
DOI: 10.1371/journal.pgen.1005011

[…] multiple alignment for each many-to-many orthogroup using t-coffee, version 10 []. each of these gene trees was then reconciled with the phylogenetic species tree for the 12 drosophila species using notung, version 2.8 []. for each input pair of gene and species trees, the reconciled tree output by notung is marked with the most parsimonious duplication and loss events along ancestral branches, […]

2014
PMCID: 4040989
PMID: 24760277
DOI: 10.1093/gbe/evu081

[…] for the transcripts of all possible pairs in a protein family using codeml (). for each protein family, a neighbor-joining tree was estimated and automatically reconciled with the species tree using notung ()., supplementary tables s1 and s2, figures s1–s7, and materials and methods are available at genome biology and evolution online (http://ww.gbe.oxfordjournals.org/)., the authors thank cindy […]

2013
PMCID: 3842944
PMID: 24312269
DOI: 10.1371/journal.pone.0081147

[…] with raxml v7.7.5 [,] using the fast bootstrapping mode and the jtt matrix model (parameters were ‘-x 12345 -p 12345 -f a -m protgammajttf’). , gene duplications and losses were evaluated with notung []. intrinsically disordered regions were analyzed with foldindex [] using a score cut-off of -0.2. phylogenetic trees were visualized with dendroscope v3 [] or e.t.e. []., publicly available […]

2011
PMCID: 3240960
PMID: 22056313
DOI: 10.1093/gbe/evr115

[…] nodes in the phylogeny with low support (<65%) prior to gene tree/species tree reconciliation. we thus reconciled all inferred gene trees with the species tree in (; ). to do so, we used notung v2.6 () to infer the most parsimonious pattern of the gene duplication and loss. gene tree nodes with less than 65% bootstrap support were treated as polytomies and allowed to rearrange […]

2010
PMCID: 2939575
PMID: 20796321
DOI: 10.1186/1471-2148-10-260

[…] with raxml version 7.2.6 [], using the gtr + i + γ model. we reconstructed an ml tree, simultaneously conducting bootstrap analysis for the best-scoring topology with 1,000 replicates., the program notung version 2.6 [,] was employed to reconcile the hatching enzyme gene tree with teleostean species tree. notung mapped duplication and loss events of the genes onto branches of the species tree […]


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Notung in publications

 (99)
PMCID: 5944053
PMID: 29743014
DOI: 10.1186/s12864-018-4744-4

[…] ml trees, with the jones, taylor and thorton (jtt) model, and 100 nonparametric bootstrap replicates []. the reconstructed bes1 gene trees were compared with real species trees by lineage using notung 2.9 software with default parameters []., orthologous and paralogous bes1 genes were identified using orthomcl (v2.0, e-value: 1e-5), and then we counted the orthologous gene pairs for each a. […]

PMCID: 5952958
DOI: 10.1093/gbe/evy081

[…] we used the software orthofinder () to obtain orthogroups (i.e., all groups of n: n orthologs) and gene trees to calculate the number of gene gain and loss events in each lineage with the program notung (). finally, we estimated the global turnover rates (β and δ) from these events using formulas 1 and 2 in , whereas the net turnover rates (δ) were directly estimated as δ = β − δ., […]

PMCID: 5901865
PMID: 29661185
DOI: 10.1186/s12915-018-0509-4

[…] trees were reconciled with the species tree, whose topology is shown in fig. , to infer the timings of gene origination, duplication, and loss. for this purpose, we iteratively employed the program notung v2.8 []. first, we ran notung with the ‘rooting’ mode, which provided a root for an unrooted tree to minimize the number of gene duplications and losses. the rooted trees were reformatted […]

PMCID: 5896119
PMID: 29642851
DOI: 10.1186/s12862-018-1147-8

[…] calculations across topologies as well as a shimodaira and hasegawa test were used to confirm that differences between likelihoods were not significant before summarizing into consensus trees., notung v.2.8.1.7 [] was utilized to reconcile the known species tree as extracted from timetree [] with the bootstrapped maximum likelihood gene tree generated by raxml including all holozoa species […]

PMCID: 5908196
PMID: 29630596
DOI: 10.1371/journal.pgen.1007322

[…] inferred when a cazyme tree topology was contradictory to the ascomycota phylogeny and could not be more parsimoniously reconciled by a combination of differential gd and gene loss. the respective notung results are given in supporting information . this analysis suggested that at least 50 (41%) of the phylogenetic pcwdcazome groups were obtained through lgts from other fungi (, supporting […]


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Notung institution(s)
Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA

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