Welcome to Sequence Flow!

Upload your alignment file or explore the example.

Upload alignment file

Select alignment type:

Include tree file

Examples

Select the dataset:

Show lines between columns

Show column numbers

Gradient links color

Merge nodes ⓘ

How to use the app?

Uploading a file

To visualize the alignment simply load your file by clicking Upload alignment file. Make sure that the alignment consists of at least two sequences. It is recommended to replace spaces in sequence names with the underscore (_), as the software used for processing the files, i.e. Biopython, tends to truncate names with whitespaces.

Sequence Flow accepts 5 MSA formats: fasta, msf, clustal, phylip, and stockholm, and allows the following file extensions: .msf, .fasta, .fna, .ffn, .faa, .frn, .fa, .clustal, .aln, .phy, .phylip, .stk, .sto, .sth, .stockholm.

After the file is loaded, select the alignment type. It is important to choose the right type because it implies the order of the nodes in the graph and cannot be changed later.

Then, click on the Visualize button.

It is possible to attach a file containing a tree in the Newick format to the visualization. To do so, check the Include tree file checkbox, and then load your file by clicking Upload Newick file.

You can also explore available examples by clicking Show example alignment.

Exploring the visualization

Your Multiple Sequence Alignment is parsed to the FASTA format. It is then represented as a graph inspired by the Partial Order Alignment model. The visualization is an interactive Sankey diagram. Read more about this concept in the ABOUT THE PROJECT section.

The app provides many features, that will help you explore the alignment, including:

Manual correction of node arrangement - you can move the nodes in columns by dragging them with your mouse
Changing the range of the visualization to a selected alignment fragment - click the left/right arrow key on your keyboard, move the scroll bar, or use the numeric inputs to see the desired alignment fragment
Customizability of view - use the checkboxes near the main visualization or click the More settings button to explore various customization options, including nodes' colouring or modifying links' appearance
Highlighting the selected subset of sequences - clicking the sequence name next to the matrix alignment representation (or phylogenetic tree, if provided), will highlight the flow of that sequence through the Sankey diagram (as well as the appropriate branch in a phylogenetic tree, if provided)
Simplifying the graph - use the Merge nodes checkbox (available for protein alignments), to aggregate the nodes in columns based on their physicochemical properties. Custom nodes grouping can be also defined inside the Vertical merging settings section

Note: Although the application lets you select any range for alignment, we recommend keeping the size within a reasonable limit. Large ranges can reduce readability, slow down browser performance, and may cause rendering issues with smaller elements. Displaying more than several hundred columns simultaneously can impact usability.

About the project

Partial Order Alignment

Partial Order Alignment (POA) is an acyclic directed graph, whose nodes are residues of the aligned sequences, and the links connect successive residues in these sequences. In addition, the set of nodes is divided into clusters, which are equivalent to the columns in the standard alignment model, with identical symbols from aligned sequences in each cluster combined into a single vertex. As a result, the aligned sequences are represented by paths in the graph, and the common nodes of these paths are their identical residues. The POA model proved useful in several applications (e.g. sequencing reads assembly and pangenome structure exploration).

Sankey Diagrams

Sankey diagram is a type of flow chart first used in 1898 to depict the energy efficiency of a steam engine, in which the width of the links is proportional to the flow rate. Sankey diagrams provide a more intuitive alignment visualization than commonly used graphical representations of nodes and links.

Sequence Flow

Sequence Flow is a tools which allows to browse interactive visualization of POAs as Sankey diagrams. It accepts multiple sequence alignment files in the most common formats, including fasta, clustal, msf, phylip, and stockholm. Sequence Flow provides integrated visualization of classic alignment, POA and phylogenetic tree. For the purpose of visualizing alignments, Sequence Flow uses SanKEY.js - a JavaScript library we developed, tailored for huge Sankey diagrams. Check out the MANUAL section for more information about the Sequence Flow features for interactive alignment exploration.

Example datasets

The service provides a couple of alignment examples, that can be interactively explored:

msl_ref7 (protein) - Dataset from BAliBASE 2 protein alignment benchmark database, reference set 7.
mucin2 (nuclein) - Dataset, which illustrates a fragment of the MUCIN_REGION_2 region (reference genome GRCh38) and 7 alternative loci. The MUCIN2 region is located on chromosome 3, with the fragment spanning positions 195702743 to 195703637.
Long reads + consensus (nucleic) - Nucleic dataset highlighting the challenges associated with long reads, which often contain multiple errors. The dataset consists of 55 reads, and their consensus sequence.
Simulated (protein, with tree) - Amino-acids-based alignment, simulated using the IQ-TREE tool. Contains phylogenetic tree.
Simulated (nucleic, with tree) - Nucleic alignment, simulated using the IQ-TREE tool. Contains phylogenetic tree.

Additional Information

The application's source code can be found in the official GitHub repository.

We appreciate every feedback. If you have experienced any issues with the app or have other suggestions, please write to: dojer@mimuw.edu.pl, or open a new issue in the repository.

Project created by Krzysztof Zdąbłasz under the supervision of Norbert Dojer, supported by Anna Lisiecka.

This work was supported by the IDUB grant of the Polish Ministry of Science and Higher Education no 01/IDUB/2019/04.