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GeneContent specifications


Unique identifier OMICS_24348
Name GeneContent
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input format TXT
Output data An inferred genome tree.
Output format PHYLIP
Operating system Unix/Linux
Computer skills Medium
Maintained No


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Publication for GeneContent

GeneContent citations


Molecular evidence for convergent evolution and allopolyploid speciation within the Physcomitrium Physcomitrella species complex

BMC Evol Biol
PMCID: 4227049
PMID: 25015729
DOI: 10.1186/1471-2148-14-158

[…] but was necessary since splitstree does not allow presentation of the data in a continuous fashion. based on this matrix (additional file : table s2), splitstree 4 [] was used to calculate genecontent distances and a bootstrapped (1,000 replicates) neighbornet., gametophores, pre-cultured for four weeks, were chopped using a razor blade in buffer (0.107 g mgcl2* 6 h2o, 0.5 g nacl, […]


Reassessment of the Listeria monocytogenes pan genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome

BMC Genomics
PMCID: 3556495
PMID: 23339658
DOI: 10.1186/1471-2164-14-47

[…] present trees based on the neighbor joining algorithm., in order to identify the impact of indels on phylogeny we built a second tree based on the presence and absence of 2953 accessory genes using genecontent []. distance between strains was calculated with the jaccard coefficient [] and a tree was inferred using the neighbor joining reconstruction method including 100 bootstrap replicates., […]


Insights into Dynamics of Mobile Genetic Elements in Hyperthermophilic Environments from Five New Thermococcus Plasmids

PLoS One
PMCID: 3543421
PMID: 23326305
DOI: 10.1371/journal.pone.0049044

[…] analysis was carried out using mega5 software ., for gene content trees, a binary (presence/absence) matrix of plasmid genes was constructed and used to calculate gene content distances with genecontent program ., we thank adeline bidault-toffin for her excellent technical assistance. we also thank anne-claire mattenet and marie chevreau for their contribution in plasmid isolation […]

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GeneContent institution(s)
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA; Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA, USA; Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, USA; Department of Mathematics and Statistics, University of West Florida, Pensacola, FL, USA
GeneContent funding source(s)
Supported by the NIH grant RO1 GM62118.

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