This server visualizes multiple sequence alignments in CLUSTAL, PIR, or PO format.
For unaligned sequences in FASTA format, the server first aligns them using POA and then visualizes them.

Input:

Enter the input data in text format:


Or click here to Upload Input Data. Then enter the name of the uploaded file:
Uploaded Filename:

Align input sequences with POA prior to visualization: Yes No
   (Check YES for FASTA-formatted input.)

    


Visualization Options:

Show Block Labels: Number of Residues    Number of Sequences     None
     For large alignments, labels may be distracting.
Hide Sequence Colors Within Blocks: Yes    No
     For large numbers of sequences, sequence colors are not useful.
Show Only Nodes: to
     POAVIZ will filter the MSA output to include only the nodes with indices in the indicated range.
Show Only Sequences with Indices: (comma delimited list, i.e. 0,1,2,4,6)
     POAVIZ will display only the listed sequences, in the specified order.
Hierarchically Order Sequences: Yes No
     POAVIZ will visually group sequences on the basis of similarity.
Show Only Consensus Sequences From PO-MSA: Yes    No
     POAVIZ interprets sequences with titles which begin with the string "CONSENS" as consensus.
Show Sequences Associated with Consensus Sequence ID: Only applies to PO input.
     POAVIZ will visualize just those sequences assigned to a given consensus.
Smooth: (Hide insertions/deletions with less than or equal to residues).
     POAVIZ will filter the input to reveal high-level alignment structure.
Mainline: (Force the sequence with index to be straight in the graph).
     POAVIZ can make sequences, such as genomic, straight.
View alignment in None FASTA PO PIR CLUSTAL POAVIZ format as well.
     If FASTA input, POAVIZ will show any format. Otherwise, it will only show input format.


Alignment Options: Only applies to FASTA input.

Interpret all residues as amino acids:    Interpret all residues as nucleotides:
     POA assumes residues in upper case are amino acids, and residues in lower case are nucleotides.
Show Only Sequences with Indices: (comma delimited list, i.e. 0,1,2,4,6)
Exclude Sequences with Indices: (comma delimited list, i.e. 0,1,2,4,6)
     POA will filter the MSA output to include or exclude the indicated sequences.
Perform Heaviest Bundling:
     POA will use the heaviest bundling algorithm to find one or more consensus sequences.
Threshold Value for Heaviest Bundling:
     The percent identity threshold for assigning a sequence to a given consensus sequence.
Show Only Consensus Sequences in the Multiple Sequence Alignment:
Fuse Aligned Nodes with the Same Residue Label:
     While building up the PO-MSA.


    

 For very large alignments, try using the smoothing function.
 POAVIZ doesn't automatically rescale the figure according to the size of the alignment.
 Try downloading the resulting GIF and rescaling it using another program.

 Data generated by POAVIZ and POA Online are deleted from the server each day at
 3:00am Pacific Time.