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ACT: Alignment, Classification and Tree Service

SILVA ACT consists of three services:

SINA Aligner

SINA (v1.2.11) will align your rRNA gene sequences accoding to the global SILVA alignment for rRNA genes. The results can be combined with any other sequences aligned by SINA or taken from the SILVA databases by concatenation of FASTA files or using the ARB MERGE tool.

SINA Search and Classify

Enabling "Search and classify" will force SINA to additionally classify your sequences with the least common ancestor (LCA) method based on the taxonomies hosted by SILVA.

Compute Tree with RAxML or FastTree

Enabling "Compute tree" will reconstruct a phylogenetic tree based on your aligned sequences, plus optionally their neighbours, using either Opens external link in new windowFastTree or Opens external link in new windowRAxML

Find and download related sequences (nearest neighbours)

Activating "Search and Classify" will return a set of sequences that have a certain identity with your submitted sequence in the SSU/LSU datasets. By adding these sequenced to the Cart they can be downloaded.

Documentation

Opens internal link in current windowSILVA ACT Tutorial

Note

The SINA aligner and classification system is currently limited to 1000 sequences of at most 6000 bases each. If your requirements exceed this limitation, get Opens internal link in current windowSINA for local installation.

When reconstructing a tree, there is a limit of 500 sequences for RAxML and 1000 sequences for FastTree. These limits include neighbour sequences, so please ensure that the number of your input sequences times the maximum number of neighbours does not exceed this limit.

Reference

Pruesse, E., Peplies, J. and Glöckner, F.O. (2012) SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Opens external link in new windowBioinformatics, 28, 1823-1829

Copyright/License Information

Users from non-academic/commercial environments should have a look at the SILVA Terms of Use/License Information