For all hyper-linked text files, copy them and then paste them
into the text box on the POAVIZ Online server.

Examples of the four input format types:
1. FASTA format for use in POA and POAVIZ:   MULTIDOM FASTA
2. PIR format for use in POAVIZ:   MULTIDOM PIR
3. CLUSTAL format for use in POAVIZ:   MULTIDOM CLUSTAL
4. PO format for use in POAVIZ:   MULTIDOM PO

To reconstruct the results in the paper:
1. Copy the text in MULTIDOM .
2. Paste it into the text box in the POAVIZ Online server.
3. Set the "Input Format" button to PIR.
4. In "Visualization Options," set the "Smooth" option to 7.
5. Click the "Visualize Alignment" button.

Protein MSA Examples from Balibase:
Alignments constructed manually using 3D structure information

For all of these examples,
Set the "Input Format" button to CLUSTAL
All options, except the consensus sequence options, apply

1. 1amk from reference 1:   1amk ref1
    Equi-distant sequences with various levels of conservation.
2. 1aboA from reference 2:   1aboA ref2
    Family with a highly divergent orphan sequence.
3. 1ubi from reference 3:   1ubi ref3
    Subgroups with <25% residue identity between groups.
4. 1dynA from reference 4:   1dynA ref4
    Sequences with N/C-terminal extensions.
5. kinase2 from reference 5:   kinase2 ref5
    Sequences with Internal Insertions.

Human Unigene EST MSA Examples:
Alignments constructed using POA

For all of these examples,
Set the "Input Format" button to PO
All options, including consensus sequence options, apply

1. Hs.123648
2. Hs.100134
3. Hs.138809
The following files are too big to be pasted in a text box
to visualize them type the words in quotes into the box that says "Uploaded Filename:"
4. "Examples/POS/Hs.100000.po"
5. "Examples/POS/Hs.5086.po"