AMPHORA specifications

Information


Unique identifier OMICS_01450
Name AMPHORA
Alternative name AutoMated PHylogenomic infeRence Application
Interface Web user interface
Restrictions to use None
Input data A metagenomic or genomic sequence file.
Input format FASTA, FASTQ
Output data An input file, a marker genes file and a results file.
Programming languages Perl, PHP, Python
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainers


  • person_outline Martin Wu <>
  • person_outline Csaba Kerepesi <>
  • person_outline Daniel Banky <>
  • person_outline Vince Grolmusz <>

Additional information


Phyla-AMPHORA: https://github.com/martinwu/Phyla_AMPHORA

Information


Unique identifier OMICS_01450
Name AMPHORA
Alternative name AutoMated PHylogenomic infeRence Application
Software type Package/Module, Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data DNA sequences
Input format FASTA
Output data Aligned markers
Output format PHYLIP, FASTAn STOCKHOLM, SELEX or CLUSTAL
Operating system Unix/Linux, Mac OS
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.0
Stability Stable
Requirements HMMER3, RAxML, Bioperl, EMBOSS
Maintained Yes

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Documentation


Maintainers


  • person_outline Martin Wu <>
  • person_outline Csaba Kerepesi <>
  • person_outline Daniel Banky <>
  • person_outline Vince Grolmusz <>

Additional information


Phyla-AMPHORA: https://github.com/martinwu/Phyla_AMPHORA

AMPHORA articles

AMPHORA citations

 (5)
2017
PMCID: 5694629

[…] validated as phylogenetic markers for (cyano) bacteria (wu and eisen, 2008, and recently used by shih et al., 2013 and komárek et al., 2014). the sequences of these proteins were mined using the automated phylogenomic inference application—amphora2 tool (wu and scott, 2012), through default settings for the bacteria option, and with a cut-off value of 1.e−10. individual alignments […]

2017
PMCID: 5641341

[…] rpll, rplm, rpln, rplp, rpls, rplt, rpma, rpob, rpsb, rpsc, rpse, rpsi, rpsj, rpsk, rpsm, rpss, smpb, and tsf; wu and scott, 2012). ncbi taxonomy ids were mapped to phylogenetic lineages given by amphora2., for the sequences’ functional characterization, we used the img/mer pipeline and tools. to further analyze the biological processes linked to the individual genes and open reading frames […]

2015
PMCID: 4681832

[…] examples of programs using these approaches are mocat (kultima et al., 2012), which uses the refmg database (ciccarelli et al., 2006) constituted by a collection of 40 single copy marker genes, and amphora (wu and eisen, 2008), which includes a database containing around 31 single copy universal markers (table 2). after the single copy marker identification, such pipelines perform an otu […]

2015
PMCID: 4477158

[…] (synechococcus sp. 65ay6a5, pe a4), and prjna210214 (synechococcus sp. 60ay4m2, pe a14)., the strain genome phylogeny was obtained using a concatenation of 460 marker proteins identified by phyla-amphora (wang and wu, 2013), which uses phylum-specific conserved proteins for metagenomic phylotyping. only conserved cyanobacterial proteins present in all five genomes (the strains studied […]

2015
PMCID: 4319941

[…] spanning 27 phyla, as provided by the software amphora2 [33]. when more than one genome was included in one genus in amphora2, we randomly selected one genome for further analysis. furthermore, amphora2 provided 31 commonly shared marker genes (s3 table) across the 426 selected representative strains (s4 table) and the 45 bifidobacterial genomes analyzed herein, and we used these 31 marker […]

AMPHORA institution(s)
Department of Biology, University of Virginia, Charlottesville, VA, USA

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