PyNAST

[…] al., 2012) with a minimum identity of 97%. taxonomy was assigned using uclust (version 1.2.22) (edgar, 2010) with the greengenes database as reference (version 13.8) and sequences were aligned using pynast (version 1.2.2) (caporaso et al., 2010a). otu’s identified in less than 0.1% of the reads were removed as well as reads identified as chloroplast or mitochondria. archaea were not filtered […]

[…] taxonomic units using the pick_open_reference_otus.py command with default parameters using the uclust method (edgar, 2010). otus occurring only once (singletons) or that failed to align using pynast were removed (caporaso et al., 2010a). relative diversity analyses were generated using the command core_diversity_analyses.py. raw sequence reads have been submitted to the sequence read […]

[…] (edgar, 2013) and the dereplicated reads were clustered into otus at a 97% sequence similarity threshold. singleton otus were removed and the remaining high-quality sequence reads were aligned with pynast (caporaso et al., 2010a) against the ribosomal database project (rdp, release 11.3)., based on the growth profiles of the cultures, three time series samples (days 1, 3, and 5) were collected […]

[…] similarity using an open reference otu picking strategy. the most abundant sequence in each otu was selected as representative sequences and further aligned against the greengenes core set using pynast software (caporaso et al., 2010). taxonomy was assigned to each otu using the ribosomal database project (rdp) classifier with a minimum confidence threshold of 80% (wang et al., 2007). […]

[…] reads using the uclust61 with a pairwise identity threshold of 0.97., representative sequences for each otu were picked using the “most–abundant” method and otu sequence alignment was performed with pynast59. the ribosomal database project (rdp)62 classifier was used for taxonomic assignment with a 95% confidence threshold. sequences with the best match for eukaryotes (i.e. chloroplasts […]