AMPHORA
{{About|an open-source bioinformatics workflow|other uses|Amphora (disambiguation)}}
{{Infobox Software
| name = AMPHORA
| logo =
| screenshot =
| caption =
| developer = Martin Wu, Jonathan Eisen et al.
| latest release version = 2.0
| latest release date = 2013
| latest preview version =
| latest preview date =
| operating system = Linux
| programming language = Perl
| language = English
| genre = 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.
{{Cite journal
| volume = 9
| issue = 10
| pages = R151
| last = Wu
| first = Martin
|author2=J.A. Eisen
| title = A simple, fast, and accurate method of phylogenomic inference.
| journal=Genome Biol.
| year = 2008
| pmc=2760878
| doi=10.1186/gb-2008-9-10-r151
| pmid=18851752
| doi-access = free
}}
{{Cite journal
| volume = 28 | issue = 7
| pages = 1033–1034
| last = Wu
| first = Martin
|author2=A.J. Scott
| title = Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2
| journal=Bioinformatics
| year = 2012
| doi=10.1093/bioinformatics/bts079
| pmid=22332237
| doi-access = free
}}
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
{{Cite journal
| volume = 304
| pages = 66–74
| last = Venter
| first = J. Craig
| title = Environmental Genome Shotgun Sequencing of the Sargasso Sea
| journal=Science
| year = 2004
| doi=10.1126/science.1093857
| issue=5667
| pmid=15001713
| bibcode = 2004Sci...304...66V
|display-authors=etal| citeseerx = 10.1.1.124.1840
| s2cid = 1454587
}}
in 2008, but recently there are more and more metagenomic datasets in the Sequence Read Archive waiting for analysis with AMPHORA2.
AmphoraNet
AmphoraNet
{{Cite journal
| volume = 533
| pages = 538–540
| last = Kerepesi
| first = Csaba
| title = The webserver implementation of the AMPHORA2 metagenomic workflow suite
| journal= Gene
| year = 2014
| pmid=24144838
| doi = 10.1016/j.gene.2013.10.015
| issue=2
|display-authors=etal}}
is the web server implementation of the AMPHORA2 workflow developed by the PIT Bioinformatics Group. AmphoraNet uses the default options of AMPHORA2.
AmphoraVizu
AmphoraVizu
{{Cite journal
| volume = 69
| issue=3
| pages = 695–697
| last = Kerepesi
| first = Csaba
| title = Visual Analysis of the Quantitative Composition of Metagenomic Communities: the AmphoraVizu Webserver
| journal= Microbial Ecology
| year = 2014
| pmid=25296554
| doi = 10.1007/s00248-014-0502-6
| s2cid=14207754
|display-authors=etal}}
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
{{reflist}}
- [https://web.archive.org/web/20160303214151/http://wolbachia.biology.virginia.edu/WuLab/Software.html Phyla
_AMPHORA]
Category:Metagenomics software