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Protocols

Phylodendron specifications

Information


Unique identifier OMICS_04259
Name Phylodendron
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 0.8
Stability Stable
Maintained Yes

Versioning


No version available

Information


Unique identifier OMICS_04259
Name Phylodendron
Interface Web user interface
Restrictions to use None
Programming languages Java
Computer skills Basic
Version 0.8
Stability Stable
Maintained Yes

Phylodendron citations

 (39)
library_books

Evolution of microRNA in primates

2017
PLoS One
PMCID: 5480830
PMID: 28640911
DOI: 10.1371/journal.pone.0176596

[…] -f a -m gtrgamma -p 12345 -x 12345 -# 1000 -s -n []. mature and excised mirna alignments were visualized with the max plank institute’s bionformatics toolkit [] and trees were visualized with phylodendron (http://iubio.bio.indiana.edu/treeapp/). trees were visually examined for evidence of potential adaptation, such as an excess of paralogs found only in a particular subgroup of primates, […]

library_books

A mouse tissue transcription factor atlas

2017
Nat Commun
PMCID: 5413951
PMID: 28429721
DOI: 10.1038/ncomms15089

[…] the distances between the rows or columns of a data matrix were computed as the euclidean distance. the ‘nuclear receptor ring of physiology' illustrated in was drawn using the application phylodendron. separations were determined using pca. for the ttmtf set, the first principal component resulting from the analysis (pc1) was the main direction that was informative for the blastoderm […]

library_books

Identification and Expression Analysis of the Complete Family of Zebrafish pkd Genes

2017
PMCID: 5318412
PMID: 28271061
DOI: 10.3389/fcell.2017.00005

[…] were generated using regions of the polycystin-cation-channel domain contained in all of the proteins (see supplementary figures , ). we used both the neighbor-joining (nj) method [plotted using phylodendron software (version 0.8d) http://iubio.bio.indiana.edu/treeapp/treeprint-form.html] and the maximum likelihood method, implementing a wag substitution model, performed using phyml […]

library_books

Agrobacterium tumefaciens estC, Encoding an Enzyme Containing Esterase Activity, Is Regulated by EstR, a Regulator in the MarR Family

2016
PLoS One
PMCID: 5201249
PMID: 28036400
DOI: 10.1371/journal.pone.0168791

[…] using espript 3.0 (http://espript.ibcp.fr/espript/cgi-bin/espript.cgi). a phylogenetic tree was constructed by the neighbor-joining method based on clustalw analysis data and displayed using phylodendron, version 0.8d (d.g. gilbert, department of biology, university of indiana, usa at http://iubio.bio.indiana.edu)., total rna was extracted from wild-type a. tumefaciens and from the estr […]

library_books

The evolutionary scope and neurological disease linkage of yeast prion like proteins in humans

2016
Biol Direct
PMCID: 4960796
PMID: 27457357
DOI: 10.1186/s13062-016-0134-5

[…] an organismal phylogeny of the eukaryotes was obtained from ncbi taxonomy []. organismal phylogenetic trees were drawn using phylot [] to generate a newick format file, which was then input into phylodendron []. orthologs in the other eukaryotes for all of the human proteins were calculated using the bi-directional best hits method, as described previously []., lists of human genes/proteins […]

library_books

Improved metagenome assemblies and taxonomic binning using long read circular consensus sequence data

2016
Sci Rep
PMCID: 4860591
PMID: 27156482
DOI: 10.1038/srep25373

[…] neighbor-joining trees were generated from the alignments using the random number generator seed of 111 and 1000 trials. the resulting phylip trees were visualized in phenogram form using the phylodendron website (iubio.bio.indiana.edu/treeapp/treeprint-form.html)., these subsets consisted of contigs totaling more than 100 kb, the minimum necessary for custom binning using phylopythias+. […]


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