PhenoGram pipeline

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


  • Invertebrates
    • Drosophila melanogaster
  • Primates
    • Homo sapiens
  • Rodents
    • 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


  • Invertebrates
    • Drosophila melanogaster
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

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Versioning


Add your version

Documentation


Maintainer


  • person_outline Daniel Wolfe <>

Publication for PhenoGram

PhenoGram IN pipelines

 (9)
2017
PMCID: 5520384
PMID: 28728544
DOI: 10.1186/s12860-017-0141-0

[…] 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 […]

2016
PMCID: 5162099
PMID: 27986076
DOI: 10.1186/s12864-016-3377-8

[…] cutoffs of eight for a di-, six for a tri-, and four for tetra-, penta-, and hexanucleotide repeats were used to report ssrs. a maximum distance of 100 bp was allowed between two ssrs. a web based phenogram [61] was used to visualize the distribution of the snp loci across the switchgrass pseudomolecules, each line representing a snp locus with its base pair coordinate., supporting data […]

2015
PMCID: 4556445
PMID: 26322511
DOI: 10.1371/journal.pone.0136771

[…] (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 […]

2015
PMCID: 4588894
PMID: 26195728
DOI: 10.1093/jxb/erv363

[…] using clustalx v.2.0.10 under the default settings (larkin et al., 2007), and the alignments used to generate a phylogenetic tree with a neighbor-joining algorithm (saitou and nei, 1987); the final phenogram was created with mega 5.0 (tamura et al., 2011). the bioinformatics program tmhmm (http://www.cbs.dtu.dk/services/tmhmm-2.0/) was used to predict transmembrane regions. sequences […]

2013
PMCID: 3662760
PMID: 23717496
DOI: 10.1371/journal.pone.0063836

[…] un-weighted pair group average method with arithmetic mean algorithm (upgma) and the neighbour program of the software package phylip 3.5. the resulting clusters were presented as dendograms (tree phenogram)., for the phylogenetic analyses, the sequence of the 6 single nuclear genes was concatenated in order to obtain a well-resolved phylogeny. concatenated single-gene sequences […]

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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