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Protocols

DendroUPGMA specifications

Information


Unique identifier OMICS_22524
Name DendroUPGMA
Alternative name Dendrogram Unweighted Pair Group Method with Arithmetic mean
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

DendroUPGMA citations

 (32)
library_books

Bifidobacteria isolated from vaginal and gut microbiomes are indistinguishable by comparative genomics

2018
PLoS One
PMCID: 5912743
PMID: 29684056
DOI: 10.1371/journal.pone.0196290

[…] binary matrix and similarities in presence/absence patterns were calculated using the Jaccard index. Dendrograms were calculated using the unweighted pair group method with arithmetic mean (UPGMA) in DendroUPGMA ([] http://genomes.urv.cat/UPGMA/index.php). […]

library_books

Chromobacterium spp. mediate their anti Plasmodium activity through secretion of the histone deacetylase inhibitor romidepsin

2018
Sci Rep
PMCID: 5906607
PMID: 29670144
DOI: 10.1038/s41598-018-24296-0

[…] nce for further assembly. Pairwise genome average nucleotide identity (gANI) was calculated using the OrthoANIu algorithm, and the resulting similarity matrix was used to generate an UPGMA tree using DendroUPGMA.The genomic sequence obtained for C. sp. Panama was then uploaded to antiSMASH v. 4. (bacterial), and the algorithm was run together with ClusterFinder for probabilistic detection of biosy […]

call_split

Differences in Virulence Between Legionella pneumophila Isolates From Human and Non human Sources Determined in Galleria mellonella Infection Model

2018
PMCID: 5893783
PMID: 29670859
DOI: 10.3389/fcimb.2018.00097
call_split See protocol

[…] mined by calculating the Pearson's coefficient with correction: d = (1 - r) x 100. Allelic profile were clustered with the Unweighted Pair Group Method with Arithmetic Averages (UPGMA), employing the DendroUPGMA computer program (http://genomes.urv.cat/UPGMA/) (Garcia-VallvĂ© and Palau, ). Phylogenetic analyses were performed using MEGA5 package (Tamura et al., ). Alignment against the correspondin […]

library_books

Phenotypic and molecular characterization of Klebsiella spp. isolates causing community acquired infections

2018
PMCID: 5913063
PMID: 29692906
DOI: 10.1016/j.nmni.2018.02.002

[…] genes were screened by PCR (): rmpA and rmpA2, entB, iroB, irp2, iucA, fimA, fimH, ecpA, ecpRAB, mrkD, mrkA, uge, urea, allS, kfuBC, cf29a, wabG and terW.A cluster analysis was performed by using the DendroUPGMA program (http://genomes.urv.cat/UPGMA/index.php?entrada=Example2), with the average linkage based on the Jacquard similarity coefficient and the respective dendrogram (constructed using U […]

library_books

Diversity and microevolution of CRISPR loci in Helicobacter cinaedi

2017
PLoS One
PMCID: 5640232
PMID: 29028814
DOI: 10.1371/journal.pone.0186241

[…] strain. The dendrogram was derived from the matrix of correlation distances by using the Jaccard similarity coefficient with the Dendro-UPGMA program (UPGMA), with a dendrogram construction utility (DendroUPGMA, http://genomes.urv.cat/UPGMA/index.php) []. CRISPRTarget (http://bioanalysis.otago.ac.nz/CRISPRTarget/crispr_analysis.html) [] was utilized to predict the presence of possible protospacer […]

library_books

Comparative genomics of Australian and international isolates of Salmonella Typhimurium: correlation of core genome evolution with CRISPR and prophage profiles

2017
Sci Rep
PMCID: 5575072
PMID: 28851865
DOI: 10.1038/s41598-017-06079-1

[…] nomes, respectively. Bootstrap analysis was performed with 1,000 replicates. Based on the presence and absence of DNA segments in the P22 pan-genome, a UPGMA tree was constructed using the web-server DendroUPGMA (http://genomes.urv.cat/UPGMA). […]

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