PhyME statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PhyME

Tool usage distribution map

This map represents all the scientific publications referring to PhyME per scientific context
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PhyME specifications


Unique identifier OMICS_06273
Name PhyME
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available

Publication for PhyME

PhyME citations


Combining phylogenetic footprinting with motif models incorporating intra motif dependencies

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

[…] next generation sequencing and the resulting avalanche of data [–].Examples 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 phyl […]


Unrealistic phylogenetic trees may improve phylogenetic footprinting

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

[…] rces, approaches for de-novo 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 learn […]


Systems analysis of cis regulatory motifs in C4 photosynthesis genes using maize and rice leaf transcriptomic data during a process of de etiolation

J Exp Bot
PMCID: 5014158
PMID: 27436282
DOI: 10.1093/jxb/erw275

[…] into three major classes: (1) methods based on position weight matrix (PWM), e.g. TRAP (), MATCH (), and SIGNAL SCAN (); (2) phylogenetic footprinting methods, e.g. FootPrinter (), Phyloscan (), and PHYME (); and (3) standard motif-finding algorithms, e.g. Gibbs sampling (), MEME (), AlignACE (), YMF (), and Weeder (). It is a common practice to combine different approaches to increase the reliab […]


Cell Interactions and Patterned Intercalations Shape and Link Epithelial Tubes in C. elegans

PLoS Genet
PMCID: 3764189
PMID: 24039608
DOI: 10.1371/journal.pgen.1003772
call_split See protocol

[…] eam of these genes and their orthologs for occurrences of the sequence RTGGGAA, which has previously been shown to be bound by LAG-1 . We conducted pairwise alignments of these upstream regions using PhyME to identify conserved sequence blocks (regions of at least 14 nt with at least 70% identity). We considered a predicted LAG-1/CSL sequence conserved if it aligned to blocks containing RTGGGAA s […]


A niched Pareto genetic algorithm for finding variable length regulatory motifs in DNA sequences

3 Biotech
PMCID: 3376862
DOI: 10.1007/s13205-011-0040-6
call_split See protocol

[…] ed the motif finding algorithm PhyloCon that takes into account both aspects, conservation among orthologous genes and co-regulation of genes within a species. Sinha et al. () developed the algorithm PhyME that was based on a probabilistic approach. This algorithm handles data from promoters of co-regulated genes and orthologous sequences. […]


Occupancy Classification of Position Weight Matrix Inferred Transcription Factor Binding Sites

PLoS One
PMCID: 3208542
PMID: 22073148
DOI: 10.1371/journal.pone.0026160

[…] of binding sites (, ). However, methods of identifying TFBS which utilize additional genomic information beyond the DNA sequence have been developed in recent years. Examples of these methods include PhyME , which utilizes phylogenetic information as part of an ab initio motif discovery process, and the approach of Chen et al. , which uses a Bayesian Network (BN) , as a classifier and a number of […]

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

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