PHACCS protocols

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PHACCS specifications

Information


Unique identifier OMICS_03529
Name PHACCS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Publication for PHACCS

PHACCS in pipelines

 (2)
2010
PMCID: 2919852
PMID: 20631792
DOI: 10.1038/nature09199

[…] mother for each family, and between all families. input viral metagenomes were pooled as necessary, e.g., for the co-twin comparison, sequences from all 3 time points from each twin were merged., phaccs calculates expected number of virotypes by estimating shannon indexes from contig spectra. to compare the results with an independent method, shannon indexes derived from cd-hit clustering […]

2005
PMCID: 1185649
PMID: 16110337
DOI: 10.1371/journal.pcbi.0010024

[…] these calculations are summarized in . similar results were obtained by venter et al. [] and breitbart et al. [], and there is also software for performing such calculations (http://phage.sdsu.edu/phaccs) []., gene finding is a fundamental goal in virtually all metagenomics projects, regardless of whether complete genome sequences can be assembled or not. if large scaffolds can be retrieved […]


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PHACCS in publications

 (25)
PMCID: 5707555
PMID: 29156552
DOI: 10.3390/v9110348

[…] [] with an assumed average phage genome length of 50 kb []. the contig spectra were then used to determine the best fitted model (i.e., lowest error) in the phage communities from contig spectrum (phaccs) package []. for the brandvlei dataset, the best fitted model was logarithmic, as it yielded the lowest error., the large terminase (terl) gene phylogram was constructed using all available […]

PMCID: 5509742
PMID: 28706283
DOI: 10.1038/s41598-017-05509-4

[…] is poor due to the paucity of available three-dimensional structural information. here we present a high-resolution crystal structure of the catalytic domain of phac from chromobacterium sp. usm2, phaccs-cat. the structure shows that phaccs-cat forms an α/β hydrolase fold comprising α/β core and cap subdomains. the active site containing cys291, asp447 and his477 is located at the bottom […]

PMCID: 5490818
PMID: 28594392
DOI: 10.3390/v9060141

[…] developed homologous virus diversity index (hvdx) [] reduce the data complexity and enhance virus classification of metagenomic datasets. these methods, similar to other analysis pipelines such as phaccs (phage communities from contig spectrum) [], can also be used to analyze the diversity of the phage community. for instance, hvdx determines the diversity of the phage community […]

PMCID: 5490804
PMID: 28538703
DOI: 10.3390/v9060127

[…] databases, numerous similarity-independent methods have arisen in order to circumvent the lack of sequence similarity in current databases []. the primary tool designed for this purpose remains phaccs (phage communities from contig spectrum), which provides estimates of the richness, evenness, and abundance of the most abundant viruses in a viral metagenome [], based on the principle […]

PMCID: 5081366
PMID: 27833560
DOI: 10.3389/fphar.2016.00411

[…] percentage is less than 0.01% (; ). metavir, virome, and ivirus are few publicly available databases ()., to assist viromics data analysis similarity-independent methods have been also developed. phaccs assesses the biodiversity of uncultured viral communities and quantifies virotypes (; ) and crass allows the simultaneous cross-assembly of all the samples in a dataset to identify shared […]


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PHACCS institution(s)
Ecole Supérieure de Biotechnologie de Strasbourg, Illkirch, France

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