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 & example data

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 10.0 2024-04-04 (all eukaryotes) only known genera with ecological assignment based on Põlme, S. et al. Fungal Diversity 105, 1–16 (2020). (zip)
Bacterial 16S amplicons	SEED2 tutorial for processing of bacterial 16S amplicons (pdf) bacterial 16S example data (zip) The most complete and up-to-date reference database for 16S (Bacteria and Archaea) based on SILVA 138.1 edited 2023-08-22 also includes mitochondria and chloroplasts (zip) Small reference dataset for 16S (Bacteria and Archaea) based on RDP release 11.5 train 18 edited 2023-08-04 (zip) Interactive workflow with resulted data
Common	SEED2 tutorial for joining of multiple separated paired-end samples (pdf) SEED2 tutorial for local BLAST reference database creation (pdf) SEED2 tutorial for estimate Alpha diversity indices (pdf)

Youtube Video Tutorials

SEED2 youtube chanel

All videos

Citations

usearch (UPARSE)	8.1.1861	clustering and chimera check (32bit)	Edgar R. C. (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods, 10: 996.
vsearch	2.4.3	clustering (64bit)	Rognes T., Flouri T., Nichols B., Quince C., Mahé F. (2016). VSEARCH: a versatile open source tool for metagenomics. PeerJ, 4, e2584.
mafft	7.222	sequence alignment	Katoh 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-join	1.1.2	joining two pair-end fastq reads	Aronesty E. (2011). ea-utils : "Command-line tools for processing biological sequencing data"; https://github.com/ExpressionAnalysis/ea-utils
ITSx	1.0.11	Internal Transcribed Spacers extraction	Bengtsson-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.
PhyML	20120412	estimate phylogenies by maximum likelihood	https://code.google.com/archive/p/phyml/
MrBayes	3.2.1	performs Bayesian inference of phylogeny	http://mrbayes.sourceforge.net/index.php
fastdist fnj	0.9	computing distance matrices constructing neigbour-joining trees	http://fastphylo.sourceforge.net/