Instalation

The latest version of SEED2 can be used as a standalone application. To install SEED2, just extract the zipped folder which contains the program binary "Seed2.exe", libraries and several external tools as blast, fastphylo, fastq-join, mafft, MrBayes, ITSx, PhyML, vsearch and usearch. Be sure that there are no spaces or ambiguous symbols in the SEED directory path - otherwise it may affect functionality of some external programs. We recommend to cite also the original external tool when you are using specific function in the SEED.

Tutorials

Fungal ITS amplicons
SEED2 tutorial for processing of fungal ITS amplicons (pdf)
fungal ITS2 example data (zip)
Reference database for fungal ITS classification based on UNITE release 7.1 2016-11-20 (plus plant and animal sequences from GenBank) (zip)
Bacterial 16S amplicons
SEED2 tutorial for processing of bacterial 16S amplicons (pdf)
bacterial 16S example data (zip)

Citations

usearch (UPARSE)8.1.1861clustering and chimera check (32bit)Edgar R. C. (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods, 10: 996.
vsearch2.4.3clustering (64bit)Rognes T., Flouri T., Nichols B., Quince C., Mahé F. (2016). VSEARCH: a versatile open source tool for metagenomics. PeerJ, 4, e2584.
mafft7.222sequence alignmentKatoh K, Asimenos G, Toh H. (2009) Multiple alignment of DNA sequences with MAFFT. In: Posada D. editor. Bioinformatics for DNA Sequence Analysis. Methods in Molecular Biology. New Jersey: Humana Press, pp. 39.
blastn
tblastx
makeblastdb
2.5.0+blastn
tblastx
creation of local databases
https://blast.ncbi.nlm.nih.gov/Blast.cgi
fastq-join1.1.2joining two pair-end fastq readsAronesty E. (2011). ea-utils : "Command-line tools for processing biological sequencing data"; https://github.com/ExpressionAnalysis/ea-utils
ITSx1.0.11Internal Transcribed Spacers extractionBengtsson-Palme J., Veldre V., Ryberg M., Hartmann M., Branco S., Wang Z., Godhe A., Bertrand Y., De Wit P., Sanchez M., Ebersberger I., Sanli K., de Souza F., Kristiansson E., Abarenkov K., Eriksson K. M., Nilsson R. H. (2013) ITSx: Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing. Methods in Ecology and Evolution, 4: 914-919.
PhyML20120412estimate phylogenies by maximum likelihoodhttps://code.google.com/archive/p/phyml/
MrBayes3.2.1performs Bayesian inference of phylogenyhttp://mrbayes.sourceforge.net/index.php
fastdist
fnj
0.9computing distance matrices
constructing neigbour-joining trees
http://fastphylo.sourceforge.net/