SINA (v1.2.12) 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.
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.
Enabling "Compute tree" will reconstruct a phylogenetic tree based on your aligned sequences, plus optionally their neighbours, using either FastTree or RAxML.
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.
The SINA aligner and classification system is currently limited to 1,000 sequences of at most 6,000 bases each. If your requirements exceed this limitation, get SINA for local installation.
When reconstructing a tree, there is a limit of 500 sequences for RAxML and 1,000 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.
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