Phylodendron protocols

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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

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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 in pipelines

 (10)
2017
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, […]

2016
PMCID: 4727409
PMID: 26809710
DOI: 10.1186/s12862-016-0594-3

[…] from ncbi taxonomy (http://www.ncbi.nlm.nih.gov). organismal phylogenetic trees were drawn using phylot (http://phylot.biobyte.de) to generate a newick format file, which was then input into phylodendron (http://iubio.bio.indiana.edu/treeapp/treeprint-form.html). orthologs for all of the s. cerevisiae proteins in all of the other fungi were calculated using the bi-directional best hits […]

2015
PMCID: 4406453
PMID: 25736599
DOI: 10.1016/j.ijpara.2015.01.004

[…] these sequences were aligned using clustalx2 and a phylogenetic tree generated using clustalw2 – phylogeny (http://www.ebi.ac.uk/tools/phylogeny/clustalw2_phylogeny/) and phylodendron (phylogenetic tree printer; http://iubio.bio.indiana.edu/treeapp/treeprint-form.html)., plasmid pnas-35, containing the c. elegans dpy-31 promoter and 3′ untranslated region (utr), […]

2015
PMCID: 4597100
PMID: 26320581
DOI: 10.1016/j.str.2015.07.018

[…] server (tcoffee.crg.cat). for phylogenetic analysis, the sequence from the set-n region to the c terminus was used, the tree was produced in t-coffee, and the tree diagram was produced using the phylodendron phylogenetic tree printer (indiana university). to generate pairwise identity/similarity statistics, the emboss-needle algorithm for pairwise sequence alignment () was used., human […]

2013
PMCID: 4222724
PMID: 24274142
DOI: 10.1186/1471-2180-13-267

[…] listed in additional file : table s2 was used to determine the ratios., protein sequences were retrieved from the ncbi database by using blastp searches. the clustal w software and the on-line tool phylodendron (http://iubio.bio.indiana.edu/treeapp/treeprint-form.html) were used for the multiple alignment and phylogenetic tree construction., w3-18-1 was shown previously to reduce fe(iii) oxide […]

Phylodendron in publications

 (34)
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, […]

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 […]

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 […]

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 […]

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 […]

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