TreeDyn protocols

View TreeDyn computational protocol

TreeDyn statistics

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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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Publication for TreeDyn

TreeDyn in pipelines

 (44)
2018
PMCID: 5822839
PMID: 29479499
DOI: 10.7717/peerj.4391

[…] the phylogenetic tree from a multiple sequence alignment of protein sequences that are representative of the longest protein-coding translation of the gene from all species compared. the program treedyn (); (http://www.phylogeny.fr) was used to visualize and annotate the phylogenetic tree., the numbers and structure of alternative transcripts were acquired by searching the ensembl database […]

2018
PMCID: 5838007
PMID: 29545816
DOI: 10.3389/fpls.2018.00257

[…] phylogenetic tree was generated through the software http://phylogeny.lirmm.fr/phylo_cgi/phylogeny.cgi, using the following pipeline: muscle for multiple alignment, phyml for tree building, and treedyn for tree rendering (). bootstrapping of 1000 was used., at5g02040, at5g05987, at3g11397, at3g56110, at2g40380, at5g05380, at2g38360, at5g01640, at5g01640, at4g29658, at1g04260, at1g08770, […]

2017
PMCID: 5298969
PMID: 28232818
DOI: 10.3389/fmicb.2017.00130

[…] regions due to gaps and poor alignment. phyml program (v3.1/3.0 alrt) was used to reconstruct tree using maximum likelihood method and final editing and graphical presentation was done using treedyn (v198.3) (; , ; ; ; ; , ). the ribbon diagram of the template and the predicted structure of pfpms1, pfmsh2-1, pfmsh2-2, and pfmsh6 were prepared using swiss-model workspace server () […]

2017
PMCID: 5316547
PMID: 28265558
DOI: 10.3389/fbioe.2017.00008

[…] the phylogeny.fr customized workflow service1 including alignment curation with gblocks2 (using default parameters), tree construction with phyml3 (using default parameters), and visualization by treedyn4 (castresana, ; chevenet et al., ; dereeper et al., ; guindon et al., ). consensus sequences of all otus are available in supplementary information, and raw sequence data are available […]

2017
PMCID: 5322194
PMID: 28280489
DOI: 10.3389/fmicb.2017.00270

[…] 20) and the validated novel micrornas as input. for multiple sequence alignment, clustalw (larkin et al., ) (version 2.1) was used with default parameters. the phylogenetic tree was plotted with treedyn (chevenet et al., ) (version 198.3) on the phylogeny.fr server (dereeper et al., ) using default settings., rna extraction was performed using the mirneasy kit (qiagen). 500 ng of rna […]


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TreeDyn in publications

 (196)
PMCID: 5923477
PMID: 29642453
DOI: 10.3390/v10040183

[…] ncbi. each phylogenetic tree was obtained through the “one click” mode of phylogeny analysis using multiple sequence comparison by log-expectation (muscle) for alignment, phyml for phylogeny, and treedyn for drawing [,]., to determine and visualize the positions of glycosylation sites, we generated 3d structures of representative ha and na proteins with different patterns of potential […]

PMCID: 5838007
PMID: 29545816
DOI: 10.3389/fpls.2018.00257

[…] phylogenetic tree was generated through the software http://phylogeny.lirmm.fr/phylo_cgi/phylogeny.cgi, using the following pipeline: muscle for multiple alignment, phyml for tree building, and treedyn for tree rendering (). bootstrapping of 1000 was used., at5g02040, at5g05987, at3g11397, at3g56110, at2g40380, at5g05380, at2g38360, at5g01640, at5g01640, at4g29658, at1g04260, at1g08770, […]

PMCID: 5828091
PMID: 29482557
DOI: 10.1186/s12934-018-0880-4

[…] phyml program v3.0 [] using the wag substitution model and 100 bootstrap replicates for inner branch accuracy. the graphical representation and edition of the phylogenetic tree was performed with treedyn v198.3 []. sequence logos were obtained using python’s weblogo package [] using the clustal omega’s alignment file as input. the scale of the logo was measured in bits, which are units […]

PMCID: 5827402
PMID: 29298888
DOI: 10.1128/JVI.01924-17

[…] aligned by muscle using clustalw (embl-ebi, hinxton). maximum likelihood trees were generated using phyml 3.1/3.0 alrt with substitution model hky85 and gblock alignment refinement (phylogeny.fr). treedyn 198.3 was used for visualization., seroprevalence of the novel rhesus adenovirus vectors was assessed by luciferase-based virus neutralization assays as previously described (). briefly, 100 […]

PMCID: 5803842
PMID: 29415650
DOI: 10.1186/s12864-018-4502-7

[…] to build a phylogenetic tree for cmrbp50-like ptbs. amino-acid sequence alignments, phylogenetic analysis and graphical representation of the phylogenetic tree were performed using t-coffee with treedyn (v198.3) (http://phylogeny.lirmm.fr/phylo_cgi/simple_phylogeny.cgi) []. in the phylogenetic tree, the branch length is proportional to the number of substitutions per site and the tree […]


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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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