AMPHORA statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

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


download.png

Versioning


No version available

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 citations

 (111)
call_split

Complete Genome Sequence of Staphylococcus haemolyticus Type Strain SGAir0252

2018
Genome Announc
PMCID: 5946035
PMID: 29748397
DOI: 10.1128/genomeA.00229-18
call_split See protocol

[…] e of 2,632,932 bp (71.3-fold coverage) and the plasmid pSGAir0252 of 41,662 bp (18.63-fold coverage). The overall G+C content was 32.78%.The Phylum-specific Automated Phylogenomic Inference Pipeline (Phyla_AMPHORA) () predicted 100% identity at the species taxonomic level. Further taxonomic assignment was investigated with the average nucleotide identity (ANI) method, using the Microbial Species I […]

library_books

GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan Genome Phylogenies, Used for a Critical Geno Taxonomic Revision of the Genus Stenotrophomonas

2018
Front Microbiol
PMCID: 5938378
PMID: 29765358
DOI: 10.3389/fmicb.2018.00771

[…] In this study we developed and benchmarked GET_PHYLOMARKERS, an open-source, comprehensive, and easy-to-use software package for phylogenomics and microbial genome taxonomy. Programs like amphora (Wu and Eisen, ) or phylosift (Darling et al., ) allow users to infer genome-phylogenies from huge genomic and metagenomic datasets by scanning new sequences against a reference database of co […]

library_books

A genetically and functionally diverse group of non diazotrophic Bradyrhizobium spp. colonizes the root endophytic compartment of Arabidopsis thaliana

2018
BMC Plant Biol
PMCID: 5896095
PMID: 29642886
DOI: 10.1186/s12870-018-1272-y

[…] The 31 AMPHORA genes were found to be present in all the assemblies. The nucleotide sequence of inidividal AMPHORA genes were aligned with Clustal Omega v. 1.2.4 [] and non-conserved segments were removed wi […]

library_books

Genome Reduction in Psychromonas Species within the Gut of an Amphipod from the Ocean’s Deepest Point

2018
mSystems
PMCID: 5893861
PMID: 29657971
DOI: 10.1128/mSystems.00009-18

[…] Marker genes were identified by AMPHORA2 (), which documents 31 marker genes selected on the basis of the construction of a genome tree of 578 bacterial species. We searched for these 31 marker genes by hmmsearch of the Pfam databas […]

call_split

Phylogenetic Diversity and Single Cell Genome Analysis of “Melainabacteria”, a Non Photosynthetic Cyanobacterial Group, in the Termite Gut

2018
PMCID: 5877343
PMID: 29415909
DOI: 10.1264/jsme2.ME17137
call_split See protocol

[…] using TXSScan ().A maximum likelihood tree was constructed using FastTree v2.1.9 () based on the concatenated amino acid sequences of a subset of the above 83 single copy gene markers, detected using AMPHORA2 software (). Concatenated sequences were then aligned using MUSCLE and edited using Gblocks. […]

library_books

Lignolytic consortium omics analyses reveal novel genomes and pathways involved in lignin modification and valorization

2018
Biotechnol Biofuels
PMCID: 5863372
PMID: 29588660
DOI: 10.1186/s13068-018-1073-4

[…] enes present within a phylogenetic lineage. Bins presenting completeness greater than 75%, contamination less than 10%, and strain heterogeneity less than 25% were selected for further analysis using Phyla-AMPHORA [], which also incorporates bacterial phylum-level phylogenetic markers for taxonomy assignment. […]

Citations

Looking to check out a full list of citations?

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