I need to align 16S rRNA gene sequences using mothur. What is the recommended mothur command for alignment, including essential parameters, and what is the latest mothur-compatible SILVA reference file version available for download, based on the blog's information?
Navigate to the mothur.org website. Go to the 'Manual' section. Navigate to the 'Sequence processing' category within the manual. Click on the 'align.seqs' command link. Identify the basic syntax and essential parameters for the 'align.seqs' command. Navigate to the 'Blog' section of the website. Locate the latest blog post related to SILVA reference files. Identify the specific version number of the SILVA database mentioned as mothur-compatible. Synthesize the alignment command details and the SILVA version.
State the primary mothur command for alignment ('align.seqs'). Provide a basic example of the 'align.seqs' command syntax, including 'fasta' and 'reference' parameters (e.g., 'mothur > align.seqs(fasta=your_sequences.fasta, reference=silva.fasta)'). Identify the latest mothur-compatible SILVA reference file version mentioned on the blog ('SILVA v138.2').