MetaPhyler specifications

Information


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

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Publication for MetaPhyler

MetaPhyler in publications

 (22)
PMCID: 5743799
PMID: 28696003
DOI: 10.1111/1751-7915.12757

[…] diversity of microbial communities, as it does not depend on the quality of contig assembly (peabody et al., ). in order to determine how this approach compared with assembled/clustered reads, metaphyler (liu et al., ), kraken (wood and salzberg, ) and nucleotide–nucleotide blast (blastn) search (altschul et al., ) were applied to mcl unassembled reads (fig. s3a–c respectively). […]

PMCID: 5490804
PMID: 28538703
DOI: 10.3390/v9060127

[…] 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 […]

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

[…] version 2.9 into chula vista viral contigs that were also included in the haloviral library ()., 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 […]

PMCID: 5037290
PMID: 27729905
DOI: 10.3389/fmicb.2016.01521

[…] are identified in the sequences of the metagenome and annotated using sequence or phylogenetic similarity to the marker gene database sequences. bioinformatics applications for this purpose include metaphyler (liu et al., ), emirge (miller et al., ), and amphora (wu and scott, ). gladden et al. () used emirge to reconstruct near full-length small subunit (ssu) rrna genes from metagenomic […]

PMCID: 4909775
PMID: 27379087
DOI: 10.3389/fmicb.2016.00965

[…] genes justifying ‘who is there?’ or protein coding sequences indicating ‘what are they doing?’ there are various types of software to taxonomically annotate the metagenomes viz. metaphlan, amphora, metaphyler, phylosift, phylotu. (2) binning, a process of grouping reads to slot them to operational taxonomic units. methods of binning are based either on compositional features or alignment […]


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

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