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AMPHORA | A method of phylogenomic inference

Allows genome tree reconstruction and metagenomic phylotyping. AMPHORA is an application for large-scale protein phylogenetic analysis. The software supports the analyses of DNA sequences, which means that users can apply AMPHORA2 directly to metagenomic reads without the need to first annotate the sequence. It can phylotype metagenomic sequences from a mixed population of bacteria and archaea and should be useful for the study of microbial evolution and ecology in the genomic era. A web application and a flavor of AMPHOR2 are also available.

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AMPHORA classification

AMPHORA specifications

Unique identifier:
OMICS_01450
Alternative names:
AMPHORA2, Phyla-AMPHORA, AmphoraNet
Restrictions to use:
None
Input format:
FASTA, FASTQ
Programming languages:
Perl, PHP, Python
Stability:
Stable
Name:
AutoMated PHylogenomic infeRence Application
Interface:
Web user interface
Input data:
A metagenomic or genomic sequence file.
Output data:
An input file, a marker genes file and a results file.
Computer skills:
Basic
Maintained:
Yes

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AMPHORA classification

AMPHORA specifications

Unique identifier:
OMICS_01450
Alternative names:
AMPHORA2, Phyla-AMPHORA, AmphoraNet
Interface:
Command line interface
Input data:
DNA sequences
Output data:
Aligned markers
Operating system:
Unix/Linux, Mac OS
License:
GNU General Public License version 2.0
Version:
2.0
Requirements:
HMMER3, RAxML, Bioperl, EMBOSS
Name:
AutoMated PHylogenomic infeRence Application
Software type:
Package/Module, Pipeline/Workflow
Restrictions to use:
None
Input format:
FASTA
Output format:
PHYLIP, FASTAn STOCKHOLM, SELEX or CLUSTAL
Programming languages:
Perl
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes

AMPHORA distribution

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AMPHORA support

Documentation

Maintainers

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

Additional information

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

Credits

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Publications

Institution(s)

Department of Biology, University of Virginia, Charlottesville, VA, USA

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