Notung pipeline

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

 (12)
2018
PMCID: 5888912
PMID: 29319812
DOI: 10.1093/molbev/msy002

[…] nodes in comparison with the topology of broadly accepted phylogenetic relationships—the species tree. for this purpose, we then conducted rearrangement analysis using a method implemented in notung (chen et al. 2000) for the nj gene tree compared with the species tree (supplementary fig. s1a4, supplementary material online). as a first step, notung rearranges weakly supported nodes […]

2018
PMCID: 5888912
PMID: 29319812
DOI: 10.1093/molbev/msy002

[…] analysis using a method implemented in notung (chen et al. 2000) for the nj gene tree compared with the species tree (supplementary fig. s1a4, supplementary material online). as a first step, notung rearranges weakly supported nodes of the gene tree to minimize duplication and extinction of genes, using parsimony with equal weights. we set the threshold to 70% for bootstrap support values […]

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

[…] alignment for each many-to-many orthogroup using t-coffee, version 10 [105]. each of these gene trees was then reconciled with the phylogenetic species tree for the 12 drosophila species using notung, version 2.8 [106]. 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 […]

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

[…] was then reconciled with the phylogenetic species tree for the 12 drosophila species using notung, version 2.8 [106]. 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, such that branches of the gene tree now coincide with speciation events of the species tree. […]

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

[…] most parsimonious duplication and loss events along ancestral branches, such that branches of the gene tree now coincide with speciation events of the species tree. each subtree of the reconciled notung tree was considered separately as a new potential orthogroup., potential orthogroups that contained fewer or greater than one d. melanogaster gene were discarded. all remaining potential […]

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

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