AMPHORA
| Developer(s) | Martin Wu, Jonathan Eisen et al. |
|---|---|
| Stable release | 2.0
/ 2013 |
| Repository | |
| 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
[edit]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
[edit]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
[edit]- ^ 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 2760878. PMID 18851752.
- ^ 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. PMID 22332237.
- ^ Venter, J. Craig; et al. (2004). "Environmental Genome Shotgun Sequencing of the Sargasso Sea". Science. 304 (5667): 66–74. Bibcode:2004Sci...304...66V. CiteSeerX 10.1.1.124.1840. doi:10.1126/science.1093857. PMID 15001713. S2CID 1454587.
- ^ 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.
- ^ 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. S2CID 14207754.
- [https://web.archive.org/web/20160303214151/http://wolbachia.biology.virginia.edu/WuLab/Software.html Phyla
_AMPHORA]