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Protocols

Phoenix specifications

Information


Unique identifier OMICS_14753
Name Phoenix
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use None
Input data A set of multiple FASTA-formatted files and matching quality files, respectively, where each FASTA file contains the sequence information from a particular sample.
Input format FASTA
Output data OTUs, taxonomic annotations, and sample relation trees
Operating system Unix/Linux, Mac OS, Windows
Programming languages Javascript, Perl
Computer skills Medium
Version 2.0
Stability Stable
Maintained Yes

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  • person_outline Jung Soh

Publication for Phoenix

Phoenix citations

 (11)
library_books

Ancient Regulatory Role of Lysine Acetylation in Central Metabolism

2017
MBio
PMCID: 5705920
PMID: 29184018
DOI: 10.1128/mBio.01894-17

[…] ly, peptides were resuspended in water, and a total of 500 ng was loaded into a trap column (5 cm by 360-µm-outer-diameter [OD] by 150-µm-inner-diameter [ID] fused silica capillary tubing [Polymicro, Phoenix, AZ]) packed with 3.6-µm Aeries C18 particles (Phenomenex, Torrance, CA). Separation was performed in a capillary column (70 cm by 360-µm OD by 75-µm ID) packed with 3-µm Jupiter C18 stationar […]

library_books

Use of Population Genetics to Assess the Ecology, Evolution, and Population Structure of Coccidioides

2016
PMCID: 4880095
PMID: 27191589
DOI: 10.3201/eid2206.151565

[…] Population structure analysis of 495 separate fungal isolates suggests at least 3 different C. posadasii subpopulations in Arizona, in agreement with PCoA data (). Clinical samples from Yuma and Phoenix (designated PHOENIX) and Tucson patients (designated TUCSON) fall in 2 different populations according to STRUCTURE (, panel B). All environmental samples and some veterinary/clinical samples […]

library_books

Spectrum of Viral Pathogens in Blood of Malaria Free Ill Travelers Returning to Canada

2016
PMCID: 4861526
PMID: 27089008
DOI: 10.3201/eid2205.151875

[…] 2 (Roche Applied Sciences, Laval, QC, Canada); Plasmodium falciparum and P. vivax small subunit rRNA DNA clones (MRA-177 and MRA-178, MR4; ATCC, Manassas VA, USA); CHIKV MBC099 AmpliRun PCR Controls (Phoenix Airmid Biomedical, Oakville, ON, Canada). We also used previously characterized in-house, positive controls (i.e., herpes simplex virus [HSV]-1 and HSV-2, cytomegalovirus [CMV], Epstein-Barr v […]

library_books

Community Structure in Methanogenic Enrichments Provides Insight into Syntrophic Interactions in Hydrocarbon Impacted Environments

2016
Front Microbiol
PMCID: 4840303
PMID: 27148240
DOI: 10.3389/fmicb.2016.00562

[…] Analysis of 16S rRNA gene pyrotag data was carried out using the Phoenix 2 pipeline (). Briefly, quality control was performed to remove low quality and chimeric sequences. Dereplication was performed (99% identity threshold) and sequences were clustered into OTUs […]

call_split

Metagenomic Analysis Indicates Epsilonproteobacteria as a Potential Cause of Microbial Corrosion in Pipelines Injected with Bisulfite

2016
Front Microbiol
PMCID: 4729907
PMID: 26858705
DOI: 10.3389/fmicb.2016.00028
call_split See protocol

[…] (Montreal, QC). Pyrosequencing was performed in a Genome Sequencer FLX Instrument, using a GS FLX Titanium Series Kit XLR70 (Roche Diagnostics Corporation). The 16S sequence reads were analyzed with Phoenix 2 (Soh et al., ). […]

call_split

Microbial Methane Production Associated with Carbon Steel Corrosion in a Nigerian Oil Field

2016
Front Microbiol
PMCID: 4707241
PMID: 26793176
DOI: 10.3389/fmicb.2015.01538
call_split See protocol

[…] sing the Invitogen Qubit fluorometer again, amplicons were sent to Genome Quebec and McGill University Innovation Centre (Montreal, QC) for 16S rRNA pyrosequencing.Analyses of data were done with the Phoenix2 software package, where data were subjected to stringent quality control (QC) checks (Soh et al., ). This included matching primer sequences, matching adaptor sequences, and removing chimeric […]


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Phoenix institution(s)
Visual Genomics Centre, Faculty of Medicine, University of Calgary, Calgary, AB, Canada; Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
Phoenix funding source(s)
This work was supported by funding from Genome Canada, Genome Alberta, the Government of Alberta and Genome BC.

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