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TREECON specifications

Information


Unique identifier OMICS_24798
Name TREECON
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The number of aligned nucleotides.
Operating system Windows
Computer skills Advanced
Stability Stable
Maintained Yes

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No version available

Additional information


http://bioinformatics.psb.ugent.be/downloads/psb/Userman/treecon_userman.html

Publication for TREECON

TREECON citations

 (116)
library_books

Indigenous Pseudomonas spp. Strains from the Olive (Olea europaea L.) Rhizosphere as Effective Biocontrol Agents against Verticillium dahliae: From the Host Roots to the Bacterial Genomes

2018
Front Microbiol
PMCID: 5829093
PMID: 29527195
DOI: 10.3389/fmicb.2018.00277

[…] eudomonas spp. type strains (retrieved from different public databases, i.e., NCBI, EMBL, KEGG, etc.,) and phylogenetically related to the three strains under studied. A dendrogram was generated with TREECON for Windows software (Van de Peer and De Wachter, ), using the Neighbor-Joining algorithm. P. entomophila L48 was used as out-group species.A second analysis was performed (1096 nt positions) […]

call_split

Effect of Dietary Chestnut or Quebracho Tannin Supplementation on Microbial Community and Fatty Acid Profile in the Rumen of Dairy Ewes

2017
Biomed Res Int
PMCID: 5804114
PMID: 29457028
DOI: 10.1155/2017/4969076
call_split See protocol

[…] rRNA gene sequences to each other and to other sequences of equivalent length retrieved from the GenBank database using the software ClustalX 2.0.11 [] to perform sequence alignment and the software TREECON 1.3b [] for the construction of the phylogenetic tree using the neighbor-joining method []. Bootstrap analysis was performed based on 1000 resamplings. […]

call_split

Comparative efficacy of locally isolated fungal strains for Pb(II) removal and recovery from water

2017
Chem Cent J
PMCID: 5736516
PMID: 29260332
DOI: 10.1186/s13065-017-0363-4
call_split See protocol

[…] e aligned sequences were used to construct a distance matrix, after the generation of 100 bootstrap sets that was subsequently used to construct a phylogenetic tree, by neighbor-joining method, using TREECON software. The partial ITS/18S rRNA gene sequences of theses isolates were submitted to GenBank to get Accession Numbers. […]

call_split

Antagonistic endophytic bacteria associated with nodules of soybean (Glycine max L.) and plant growth promoting properties

2017
PMCID: 5914205
PMID: 29117917
DOI: 10.1016/j.bjm.2017.06.007
call_split See protocol

[…] ences were matched with ClustalX1.81 software, imported into Bioedit 4.8.4, and manually corrected. A phylogenetic tree was constructed using the Jukes–Cantor model and the neighbor-joining method in TREECON package (version 1.3b). The similarity of each tested strain was computed by using the DNAMAN application (version 6.0.3.40, Lynnon Corporation). The acquired 16S rRNA gene sequences were subm […]

library_books

No obvious genetic erosion, but evident relict status at the westernmost range edge of the Pontic‐Pannonian steppe plant Linum flavum L. (Linaceae) in Central Europe

2017
Ecol Evol
PMCID: 5574788
PMID: 28861254
DOI: 10.1002/ece3.2990

[…] A genetic distance analysis based on the complementary value of Nei and Li's similarity coefficient (Nei & Li, ) was performed with TreeCon (version 1.3b; Van de Peer & De Wachter, ; http://bioinformatics.psb.ugent.be/software/details/Treecon). The visualization of the distance matrix resulted in an unrooted neighbor‐net phenogram […]

library_books

Genetic structuring, dispersal and taxonomy of the high alpine populations of the Geranium arabicum/kilimandscharicum complex in tropical eastern Africa

2017
PLoS One
PMCID: 5446165
PMID: 28552970
DOI: 10.1371/journal.pone.0178208

[…] ze the clustering.A Neighbor-Net diagram [] was constructed based on uncorrected p-distance using SplitsTree4 v. 4.12.6 [], and support for branches was estimated from 1000 bootstrap replicates using TreeCon version 1.3b []. Analyses of Molecular Variance (AMOVAs) were performed to investigate partitioning of genetic variation at hierarchical and non-hierarchical levels using ARLEQUIN v. 3 []. Sig […]

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