2.6.4 Tools Menu

• Align/Assemble - see section 9.2 and section 10 respectively
• Tree - see section 12
• Primers - see section 13
• Cloning - see section 14
• BLAST - Perform a BLAST search (such as NCBI Blast) to find sequences that are similar to the currently selected sequence(s). See section 15
• Add/Remove Databases - options for setting up and configuring NCBI and custom BLAST, see section 15.5.3 .
• Extract Annotations - see section 8.1.4 .
• Mask Alignment - see section 9.4 .
• Concatenate Sequences or Alignments - see section 5.3.1 .
• Generate Consensus Sequence - see section 9.5 .
• Workflows - access built-in Workflows and create new ones, see chapter 16 .
• Plugins - Takes you to the Plugins menu where you can install or uninstall plugins.
• Preferences - see section 1.2.1

Many plugin options will also appear in this menu when installed, such as Classify Sequences (Sequence Classifier plugin), and Submit to Genbank (Genbank submission plugin)