TreeDyn protocols

TreeDyn specifications


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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Publication for TreeDyn

TreeDyn IN pipelines

PMCID: 5773217
PMID: 29346417
DOI: 10.1371/journal.ppat.1006765

[…] ( with default settings [41,42] was used for multiple sequence alignment (muscle; [43]), phylogenetic analysis (phyml; [44]), and tree rendering (treedyn; [45]) of uxt1 and uxt2 and other nsts. these included transporters of udp-galf (aspergillus fumigatus, af), udp-xyl (homo sapiens, hs, uxt np_116215.1; arabidopsis thaliana, at, uxt1 […]

PMCID: 5775359
PMID: 29352135
DOI: 10.1038/s41598-018-19526-4

[…] is based on a built-in pipeline with chaining programs with recognized accuracy as follow: muscle for multiple alignment70, gblocks for alignment refinement71, phyml for tree building72, and treedyn for tree rendering73. all parameters are set up to default, as they are suitable for the investigated virus69., amino acid sequences corresponding to rna polymerase from both flavivirus […]

PMCID: 5790919
PMID: 29382737
DOI: 10.1128/mBio.02319-17

[…] homo sapiens (accession no. np_055954.1), and drosophila melanogaster (accession no. np_524126.1). multiple-sequence alignment (muscle [59]), phylogenetic analysis (phyml [60]), and tree rendering (treedyn [61]) of uut1, characterized udp-glca transporters (listed above), and other known cryptococcal nucleotide sugar transporters (nsts) was done using the online program […]

PMCID: 5854309
PMID: 29543834
DOI: 10.1371/journal.pone.0193760

[…] [30] using the wag substitution model, bootstrap supports with 500 replicates and default parameters. tree was carried out using maximum likelihood and the phylogenetic tree was visualized with treedyn [31]. theoretical isoelectric point (pi) and molecular weight (mw) were calculated with the compute pi/mw tool ( putative transcription factor binding sites (tfbss) […]

PMCID: 5300976
PMID: 28239369
DOI: 10.3389/fmicb.2017.00172

[…] muscle (edgar, 2004) and then curated by the program g-block (castresana, 2000). a neighbor-joining phylogenetic tree was then determined using phyml 3.0 (anisimova and gascuel, 2006) followed by treedyn (chevenet et al., 2006), and the statistical robustness of the analysis was estimated by bootstrapping with 1,000 replicates., all sequences obtained in this study were deposited in genbank, […]

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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