AMPHORA

This article is about an open-source bioinformatics workflow. For other uses, see Amphora (disambiguation).
AMPHORA
Developer(s) Martin Wu, Jonathan Eisen et al.
Stable release
2.0 / 2013
Written in Perl
Operating system Linux
Available in English
Type Bioinformatics
License GNU General Public License
Website http://wolbachia.biology.virginia.edu/WuLab/Software.html

AMPHORA ("AutoMated Phylogenomic infeRence Application") is an open-source bioinformatics workflow.[1][2] AMPHORA2 uses 31 bacterial and 104 archaeal phylogenetic marker genes for inferring phylogenetic information from metagenomic datasets. Most of the marker genes are single copy genes, therefore AMPHORA2 is suitable for inferring the accurate taxonomic composition of bacterial and archaeal communities from metagenomic shotgun sequencing data.

First AMPHORA was used for re-analysis of the Sargasso Sea metagenomic data [3] in 2008, but recently there are more and more metagenomic datasets in the Sequence Read Archive waiting for analysis with AMPHORA2.

AmphoraNet

AmphoraNet [4] is the web server implementation of the AMPHORA2 workflow developed by the PIT Bioinformatics Group. AmphoraNet uses the default options of AMPHORA2.

AmphoraVizu

AmphoraVizu [5] is a web server developed by the PIT Bioinformatics Group which is capable to visualize outputs generated by the AMPHORA2 or its webserver implementation AmphoraNet.

References

  1. ↑ Wu, Martin; J.A. Eisen (2008). "A simple, fast, and accurate method of phylogenomic inference.". Genome Biol. 9 (10): R151. doi:10.1186/gb-2008-9-10-r151. PMC 2760878Freely accessible. PMID 18851752.
  2. ↑ Wu, Martin; A.J. Scott (2012). "Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2". Bioinformatics. 28 (7): 1033–1034. doi:10.1093/bioinformatics/bts079.
  3. ↑ Venter, J. Craig; et al. (2004). "Environmental Genome Shotgun Sequencing of the Sargasso Sea". Science. 304 (5667): 66–74. doi:10.1126/science.1093857. PMID 15001713.
  4. ↑ Kerepesi, Csaba; et al. (2014). "The webserver implementation of the AMPHORA2 metagenomic workflow suite". Gene. 533 (2): 538–540. doi:10.1016/j.gene.2013.10.015. PMID 24144838.
  5. ↑ Kerepesi, Csaba; et al. (2014). "Visual Analysis of the Quantitative Composition of Metagenomic Communities: the AmphoraVizu Webserver". Microbial Ecology. 69 (3): 695–697. doi:10.1007/s00248-014-0502-6. PMID 25296554.
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