Creating consensus and template alignments on DNA / RNA sequences

  • Updated

You can create pairwise and multisequence template alignments and consensus alignments on Benchling. To create an alignment, open the DNA / RNA alignment modal, select your inputs, then define your parameters. To learn more about plasmid alignments, visit Plasmid alignments.

Open the DNA / RNA Alignment modal

You can open the modal three ways:

  • Expanded view: In the expanded view, select the sequences you want to align, then click the More drop-down menu. Under Analyze, select Create DNA / RNA Alignment.

  • From a DNA / RNA sequence: Open an existing DNA / RNA sequence, click Alignments in the right-side menu, then click Create New Alignment.

  • Global create: Click the + icon in the left-side menu. Under DNA / RNA Sequence, select New Alignment.

The example in the screenshot below shows how to create an alignment from the expanded view.

Selecting inputs

In the DNA / RNA alignment modal, you can upload inputs from your computer, select inputs from existing Benchling files, or manually enter bases. View selected inputs in the Sequences section at the bottom of the modal.

Note: Files uploaded within the alignment modal and manually typed bases aren’t uploaded as new entities to your Benchling environment. They are stored as data on the alignment only.

Click Next in the bottom-right corner to define your parameters.

Defining parameters

Under Define parameters, you can choose between these alignment types:

  • Pairwise

  • Multisequence

  • Consensus

Pairwise template alignments make one alignment against the template for each non-template sequence.


Multi-sequence template alignments attach multiple sequences as a single alignment on the template sequence.


Consensus alignments logically populate alignment groups containing the selected sequences.

Consensus alignment


Contig consensus alignment

Pairwise and multisequence template alignments

  1. Search for and select your template and non-template sequences.

    • For alignments created through the entity’s Alignment tool, Benchling logically pre-populates an alignment group for your selected inputs. The first input is the template and the remaining inputs are non-template sequences. You can edit or remove pre-populated groups as needed.

  2. Click + next to Templates to define additional templates for creation of multiple alignment groups.

    • In a pairwise alignment, each sequence in the alignment group is aligned against the template independently.

    • In a multisequence alignment, sequences in the alignment group are aligned together with the template.

Consensus alignments

  1. Search for and select your consensus alignment sequences.

  2. Click + next to Group(s) to create groups that correspond to each consensus sequence you're creating, then add the inputs into each group.

    • Benchling logically pre-populates an alignment group containing the selected sequences from the previous step.

Change program-specific parameters and complete the alignment

Select an alignment program from the drop-down menu at the bottom of the modal. We currently support these alignment programs for consensus alignments:

Alignment program


MAFFT 6-mer distance

Uses 6-mer distance for constructing the guide tree

MAFFT auto

Picks a MAFFT strategy automatically based on the count and size of inputs.

MAFFT local pairwise

Compute local pairwise alignments using Smith-Waterman for constructing the guide tree and iterative refinement. This program may generate better results for contig alignments where multiple overlapping reads are aligned

MAFFT global pairwise

Compute global pairwise alignments using Needleman-Wunsch for constructing the guide tree and iterative refinement

Clustal Omega multiple sequence alignment

Uses seeded guide trees and HMM profile-profile techniques

You can view and change program-specific parameters, like maximum guide tree iterations, gap open penalty, and gap extension penalty before completing the alignment. To change these parameters, click Show Parameters at the bottom of the modal.

To complete the alignment:

  1. Click Create Alignment at the bottom right of the modal.

  2. After the alignments complete, click Open or View from the pop-up window to access your alignment.

    • If you created a single consensus alignment, the completed consensus alignment file opens automatically.

    • If you created a pairwise or multisequence alignment or multiple consensus alignments, the search directory opens, where you can find the list of completed alignments.

Tip: Benchling automatically trims trace files to where the peaks start to look clean. You can also manually select the trimming bar and move it with your mouse.

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