PhyloGibbs statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Motif discovery chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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 No

Versioning


Add your version

Maintainer


This tool is not available anymore.

Information


Unique identifier OMICS_06274
Name PhyloGibbs
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained No

Maintainer


This tool is not available anymore.

Publication for PhyloGibbs

PhyloGibbs in publications

 (35)
PMCID: 5550003
PMID: 28753602
DOI: 10.1371/journal.pcbi.1005176

[…] motifs. as part of its motif analysis, crunch extracts orthologous sequences from 6 other mammalian species for each peak sequence and multiply aligns these using t-coffee []. the motif finder phylogibbs [] is then run on these alignments to infer pswm motifs. crunch further refines these motifs on the multiple alignments of the training sequences using motevo []. for each dataset, we use […]

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

[…] 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 […]

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

[…] motif discovery based on phylogenetic 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 […]

PMCID: 4808798
PMID: 26751491
DOI: 10.3390/biom6010004

[…] []. 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 […]

PMCID: 4613772
PMID: 26482678
DOI: 10.1186/s12862-015-0499-6

[…] 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 […]


To access a full list of publications, you will need to upgrade to our premium service.

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

PhyloGibbs reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review PhyloGibbs