PhenoGram specifications

Information


Unique identifier OMICS_11755
Name PhenoGram
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input format text
Output data Images
Output format PNG, JPG, PDF
Programming languages Ruby
License GNU General Public License version 3.0
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Animals
    • Drosophila melanogaster
    • Homo sapiens
    • Mus musculus

Documentation


Maintainer


  • person_outline Daniel Wolfe <>

Information


Unique identifier OMICS_11755
Name PhenoGram
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input format text
Output data Images
Output format PNG, JPG, PDF
Operating system Unix/Linux, Mac OS, Windows
Programming languages Ruby
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements RMagick
Maintained Yes

Taxon


  • Animals
    • Drosophila melanogaster
    • Homo sapiens
    • Mus musculus

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Daniel Wolfe <>

PhenoGram article

PhenoGram citations

 (5)
2017
PMCID: 5520384

[…] greater than 90% were retrieved, aligned with the sequence of strain mrcj-314 (die-10), using clustal w module of mega6 software further subjected to neighbor-joining (nj) analysis to obtain the phenogram (fig. 2). the its sequence of strain (mrcj-314) die-10 has highest nucleotide similarities with cladosporium cladosporioides (eu497597), formed a clade with 100% bootstrap support […]

2017
PMCID: 5574788

[…] treecon (version 1.3b; van de peer & de wachter, 1994; http://bioinformatics.psb.ugent.be/software/details/treecon). the visualization of the distance matrix resulted in an unrooted neighbor‐net phenogram using splitstree4 (version 4.11.3; huson & bryant, 2006; http://www.splitstree.org/)., to determine genetic structure, we used bayesian clustering running baps (version 3.2.; corander, […]

2016
PMCID: 5133618

[…] resulting p-values were corrected using the bonferroni method to accommodate bias due to multiple comparisons., the chromosomal distribution and duplication state of the genes was visualised using phenogram (http://visualization.ritchielab.psu.edu/phenograms/plot - © 2012 ritchie lab)82. the predicted exon–intron structure was retrieved from the v1 annotation of the grapevine genome […]

2015
PMCID: 4556445

[…] (100% according to the wgencodecrgmapabilityalign100mer track on the ucsc genome browser), and the inserted sequence has a length greater than 300nt. fig a in s1 file visualizes these using the phenogram software [15]. these filters are intended to select a set of alleles which have the best potential to be detected with illumina sequencing. alleles that are embedded in repeats would […]

2012
PMCID: 3477124

[…] neighbor to generate 1000 neighbor joining trees. the phylip program consense was then used to generate a consensus tree with bootstrap support values and the program drawtree produced an unrooted phenogram of the consensus tree., structure was used to determine the most likely number of genetic clusters represented by the data. ten runs with the default settings (i.e. with correlated allele […]

PhenoGram institution(s)
Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Eberly College of Science, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
PhenoGram funding source(s)
This work was supported by the following funding agencies and grants: 5U01 HG004798-03, 5R01 LM010040-02, and U19 HL065962-10.

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