TreeDyn specifications

Information


Unique identifier OMICS_04270
Name TreeDyn
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 2.0
Computer skills Medium
Stability Stable
Maintained Yes

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TreeDyn article

TreeDyn citations

 (13)
2017
PMCID: 5388652

[…] used several bioinformatic programs, coordinated using the http://www.phylogeny.fr/ bioinformatic portal, to enable alignment (muscle), curation (gblocks), phylogeny (phyml) and tree rendering (treedyn), to reconstruct phylogenetic relationships (dereeper et al. 2008). sequences were identified as vertebrate ids members and a proposed primordial drosophila melanogaster ids gene and protein […]

2017
PMCID: 5398709

[…] 3.1/3.0 (arlt) software was used to assess the clade support, by computing the maximum likelihood tree and alrt test (approximate likelihood ratio test) [42]. finally the tree was drawn using the treedyn 198.3 software [43]., the work described in this manuscript is in no way linked (directly or indirectly) to ethical concerns. no data from humans have been collected. all research activities […]

2017
PMCID: 5754980

[…] support value and a number of bootstrap <50% and 85% were collapsed, respectively. the maximum likelihood method using phyml 3.0 software was utilized to construct the phylogenetic tree.[24] treedyn was used to draw and render the tree., the mic profile of ampicillin and erythromycin (himedia, india) was determined by microdilution method. twenty-four-well microtiter plate was used, 1 ml […]

2016
PMCID: 4871892

[…] test analysis was performed using phyml 3.0 with bootstrap 100 analysis (www.phylogeny.fr/one_task.cgi?task_type=phyml) using default settings. dendrograms were constructed in newick format using treedyn 198.3 (www.phylogeny.fr/one_task.cgi?task_type=treedyn). nucleotide sequences of meca and ccrb genes determined in this study were submitted to genbank under accession numbers […]

2016
PMCID: 4786556

[…] comparison by log-expectation (muscle) and the phylogeny was ascertained using phyml with alrt (approximate likelihood-ratio test) or bootstrap analysis for branches. the tree was rendered using treedyn. the numbers next to each node, in red, represent a measure of support for the node, where 1 represents maximal support. these have been computed by bootstrapping analyses., the isolated pure […]

TreeDyn institution(s)
Laboratoire de Génétique et Evolution des Maladies Infectieuses, UMR CNRS/IRD 2724, IRD, Montpellier, France; Institut de Biologie du Développement de Marseille-Luminy, CNRS UMR 6216, Parc Scientifique et Technologique de Luminy, Marseille, France; Laboratoire de Biologie Virtuelle, CNRS UMR 6543, Université de Nice Sophia Antipolis, Centre de Biochimie, Campus Valrose Nice, France

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