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MetaPhyler specifications


Unique identifier OMICS_01455
Name MetaPhyler
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained No




No version available


This tool is not maintained anymore.

Publication for MetaPhyler

MetaPhyler citations


TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganisms

BMC Genomics
PMCID: 5644092
PMID: 29037173
DOI: 10.1186/s12864-017-4168-6

[…] mic profiler that uses non-redundant signature databases for prokaryotic and viral genomes. Genometa [] is a Java program to identify bacterial species and gene content from high-throughput datasets. MetaPhyler [] estimates bacterial composition from metagenomic samples.Others use a subset of the sequences for taxonomic profiling of metagenomes. Web-based solutions are provided by MG-RAST [] and E […]


Relative abundance of ‘Candidatus Tenderia electrophaga’ is linked to cathodic current in an aerobic biocathode community

PMCID: 5743799
PMID: 28696003
DOI: 10.1111/1751-7915.12757

[…] Filtered unassembled metagenomic reads for each sample were analysed using blastn (Camacho et al., ), kraken v0.10.5‐beta(Wood and Salzberg, ) and metaphyler v1.25 (Liu et al., ). blastn analysis was performed by reporting the top five hits for each sequence from the entire NCBI database. An expectation cut‐off score of 0.001 was used. Blastn re […]


Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches

PMCID: 5490804
PMID: 28538703
DOI: 10.3390/v9060127

[…] gnment of the virome against reference databases using BLAST (Basic Local Alignment Search Tool), or BLAST-based programs such as MG-RAST (MetaGenomic-Rapid Annotation using Subsystem Technology) [], MetaPhyler [], or CARMA [], which is a time-consuming process. Alternatively, rapid fast k-mer algorithms may be applied to reduce the time associated with such analyses [,]. These algorithms are more […]


Intriguing Interaction of Bacteriophage Host Association: An Understanding in the Era of Omics

Front Microbiol
PMCID: 5383658
PMID: 28439260
DOI: 10.3389/fmicb.2017.00559

[…] cal profiling of viral communities without requiring assembly and annotation. To elucidate sequence matches with a reference database, BLAST is regularly employed along with MG-RAST (Glass et al., ), MetaPhyler (Liu et al., ) or CARMA (Gerlach et al., ). For a taxonomy of viruses, MEGAN (Huson et al., ) software can be used whereas Hidden Markov Models, e.g., HMMER (Finn et al., ) are applied to m […]


Determining virus host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics

PMCID: 5228507
PMID: 28097058
DOI: 10.7717/peerj.2844

[…] The selected individual metagenomes ( and ) were profiled for relative taxonomic abundances with MetaPhyler (). MetaPhyler aligns reads against a library of clade-specific marker genes. Reads that align against a marker gene above a particular threshold alignment score are then binned to the corr […]


MetaCRAST: reference guided extraction of CRISPR spacers from unassembled metagenomes

PMCID: 5592083
PMID: 28894651
DOI: 10.7717/peerj.3788
call_split See protocol

[…] ther the total CPU time).Similarly, CRISPR spacers were also detected by the aforementioned three tools in real AMD and EBPR metagenomes () downloaded from iMicrobe () and taxonomically profiled with MetaPhyler (). MetaCRAST analyses of the real metagenomes were performed with taxonomy- or assembly-guided query DRs generated as follows. To make an assembly-guided query, CAP3-assembled contigs () w […]

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MetaPhyler institution(s)
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, USA

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