Csaba Kerepesi1, Dániel Bánky, Vince Grolmusz. 1. PIT Bioinformatics Group, Eötvös University, H-1117 Budapest, Hungary. Electronic address: kerepesi@pitgroup.org.
Abstract
MOTIVATION: Metagenomics went through an astonishing development in the past few years. Today not only gene sequencing experts, but numerous laboratories of other specializations need to analyze DNA sequences gained from clinical or environmental samples. Phylogenetic analysis of the metagenomic data presents significant challenges for the biologist and the bioinformatician. The program suite AMPHORA and its workflow version are examples of publicly available software that yields reliable phylogenetic results for metagenomic data. RESULTS: Here we present AmphoraNet, an easy-to-use webserver that is capable of assigning a probability-weighted taxonomic group for each phylogenetic marker gene found in the input metagenomic sample; the webserver is based on the AMPHORA2 workflow. Since a large proportion of molecular biologists uses the BLAST program and its clones on public webservers instead of the locally installed versions, we believe that the occasional user may find it comfortable that, in this version, no time-consuming installation of every component of the AMPHORA2 suite or expertise in Linux environment is required. AVAILABILITY: The webserver is freely available at http://amphoranet.pitgroup.org; no registration is required.
MOTIVATION: Metagenomics went through an astonishing development in the past few years. Today not only gene sequencing experts, but numerous laboratories of other specializations need to analyze DNA sequences gained from clinical or environmental samples. Phylogenetic analysis of the metagenomic data presents significant challenges for the biologist and the bioinformatician. The program suite AMPHORA and its workflow version are examples of publicly available software that yields reliable phylogenetic results for metagenomic data. RESULTS: Here we present AmphoraNet, an easy-to-use webserver that is capable of assigning a probability-weighted taxonomic group for each phylogenetic marker gene found in the input metagenomic sample; the webserver is based on the AMPHORA2 workflow. Since a large proportion of molecular biologists uses the BLAST program and its clones on public webservers instead of the locally installed versions, we believe that the occasional user may find it comfortable that, in this version, no time-consuming installation of every component of the AMPHORA2 suite or expertise in Linux environment is required. AVAILABILITY: The webserver is freely available at http://amphoranet.pitgroup.org; no registration is required.
Authors: Rebecca-Ayme Hughes; Yunlong Zhang; Ran Zhang; Philip G Williams; Jonathan S Lindsey; Eric S Miller Journal: Appl Environ Microbiol Date: 2017-09-15 Impact factor: 4.792
Authors: Sunil Thomas; Jacques Izard; Emily Walsh; Kristen Batich; Pakawat Chongsathidkiet; Gerard Clarke; David A Sela; Alexander J Muller; James M Mullin; Korin Albert; John P Gilligan; Katherine DiGuilio; Rima Dilbarova; Walker Alexander; George C Prendergast Journal: Cancer Res Date: 2017-03-14 Impact factor: 12.701
Authors: Rebecca L Mickol; Brian J Eddie; Anthony P Malanoski; Matthew D Yates; Leonard M Tender; Sarah M Glaven Journal: Appl Environ Microbiol Date: 2021-10-06 Impact factor: 5.005
Authors: Paul G Livingstone; Oliver Ingleby; Susan Girdwood; Alan R Cookson; Russell M Morphew; David E Whitworth Journal: Appl Environ Microbiol Date: 2020-01-07 Impact factor: 4.792