AMPHORA protocols

AMPHORA specifications

Information


Unique identifier OMICS_01450
Name AMPHORA
Alternative names AutoMated PHylogenomic infeRence Application, AMPHORA2, Phyla-AMPHORA, AmphoraNet
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 names AutoMated PHylogenomic infeRence Application, AMPHORA2, Phyla-AMPHORA, AmphoraNet
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

Download


Versioning


Add your version

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

Publications for AutoMated PHylogenomic infeRence Application

AMPHORA IN pipelines

 (10)
2017
PMCID: 5694629
PMID: 29184540
DOI: 10.3389/fmicb.2017.02132

[…] 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: 5694629
PMID: 29184540
DOI: 10.3389/fmicb.2017.02132

[…] 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 were performed for each of the 31 gene sets […]

2017
PMCID: 5739016
PMID: 29028004
DOI: 10.1038/ismej.2017.162

[…] were collected (supplementary table s2). genome completeness of each downloaded genome was estimated based on the presence of 104 single-copy archaeal-specific phylogenetic marker genes using the amphora2 software package (wu and scott, 2012). only genomes with >50% of the phylogenetic marker genes present in the assembly were included to reduce bias from low-coverage genomes (n=584; […]

2017
PMCID: 5812542
PMID: 28334407
DOI: 10.1093/femsec/fix028

[…] values presented are rpms., several annotation methods were used for functional and taxonomic predictions of proteins on scaffolds >1 kb. taxonomic assignments of the genome bins were based on amphora2 classification (wu and scott 2012). bins were assigned to the highest confidence taxonomic level where 75% of the marker genes in the bin had an average confidence interval above 90. […]

2015
PMCID: 4319941
PMID: 25658111
DOI: 10.1371/journal.pone.0117912

[…] the average value of the identity., to build a complete bacterial phylogenetic tree, we selected 426 representative genomes of different genera 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 […]

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

AMPHORA reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review AMPHORA