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PhyloGibbs specifications

Information


Unique identifier OMICS_06274
Name PhyloGibbs
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Mikhail Pachkov

Information


Unique identifier OMICS_06274
Name PhyloGibbs
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Mikhail Pachkov

Publication for PhyloGibbs

PhyloGibbs citations

 (35)
library_books

Combining phylogenetic footprinting with motif models incorporating intra motif dependencies

2017
BMC Bioinformatics
PMCID: 5333389
PMID: 28249564
DOI: 10.1186/s12859-017-1495-1

[…] es for highly popular phylogenetic footprinting tools that have been applied to eukaryotes and prokaryotes are FootPrinter [], PhyME [], MONKEY [], MicroFootprinter [], Phylogenetic Gibbs Sampler [], PhyloGibbs [], PhyloGibbs-MP [], or MotEvo [].In summary, one-species approaches neglect phylogenetic information, whereas phylogenetic footprinting, which incorporates this information, neglects intr […]

library_books

Unrealistic phylogenetic trees may improve phylogenetic footprinting

2017
Bioinformatics
PMCID: 5447242
PMID: 28130227
DOI: 10.1093/bioinformatics/btx033

[…] footprinting have become increasingly attractive. Examples of highly popular tools for phylogenetic footprinting are FootPrinter (), PhyME (), MONKEY (), PhyloGibbs (), Phylogenetic Gibbs Sampler (), PhyloGibbs-MP () and MotEvo (). provides a comparison of these tools regarding the used evolutionary model, sequence model and learning principle.One prerequisite for most phylogenetic footprinting a […]

library_books

Guardian of Genetic Messenger RNA Binding Proteins

2016
Biomolecules
PMCID: 4808798
PMID: 26751491
DOI: 10.3390/biom6010004

[…] es []. PARalyzer is another popular peak calling algorithm for PAR-CLIP datasets only. Finally, motif recognition algorithms are used to identify motifs recognized by RBP. Algorithms such as MEMEris, PhyloGibbs, RNAcontext, and RNAmotifs identify motifs at the RNA level, while MEME, cERMIT, GLAM2, and MatrixREDUCE were developed to identify motif at the DNA level. Lastly, the identified RBP motif […]

library_books

Analysis of 5’ gene regions reveals extraordinary conservation of novel non coding sequences in a wide range of animals

2015
BMC Evol Biol
PMCID: 4613772
PMID: 26482678
DOI: 10.1186/s12862-015-0499-6

[…] using the SeqLogo [] package in R. All genes and organisms used in this analysis can be found in Additional file : Table S9.The motif elicitation analysis was repeated using a phylogeny-aware method, Phylogibbs []. The motif-based alignments produced by MAST [] were cut to 17 sequences due to memory constraints, and used as inputs for the algorithm. Phylogenetic trees were constructed using diverg […]

library_books

High throughput characterization of protein–RNA interactions

2014
Brief Funct Genomics
PMCID: 4303715
PMID: 25504152
DOI: 10.1093/bfgp/elu047

[…] onsider the RNA sequence, or by considering RNA secondary structure either explicitly or as a layer on top of sequence preference. The basic approaches are summarized in . The DNA-based methods MEME, PhyloGibbs and cERMIT have been used to identify motifs from RIP-chip (both raw, and filtered to include only sequences with enriched hexamers), CLIP-seq and PAR-CLIP data [, , ]. Despite ignoring sec […]

library_books

Evolution of Chloroplast Transcript Processing in Plasmodium and Its Chromerid Algal Relatives

2014
PLoS Genet
PMCID: 3894158
PMID: 24453981
DOI: 10.1371/journal.pgen.1004008

[…] alignment, and with three online motif search programs: Bioprospector (http://robotics.stanford.edu/~xsliu/BioProspector/), Improbizer(http://users.soe.ucsc.edu/~kent/improbizer/improbizer.html), and PhyloGibbs(http://www.phylogibbs.unibas.ch/cgi-bin/phylogibbs.pl). GC contents were plotted using the crude alignments and GeneIOUS Pro (http://www.geneious.com/). Conserved secondary structures were […]

Citations

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PhyloGibbs institution(s)
Center for Studies in Physics and Biology, The Rockefeller University, New York, NY, USA

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