Purpose: This tool aligns two alignments to each other. It can also synchronize a single alignment with a standard HIV reference alignment.
Details: If there is a sequence that is common to both alignments, you can specify that the tool should use this sequence as a reference. If the two alignments do not share a common sequence, the tool chooses the longest sequence from each alignment as references, then aligns them to each another. The tool then adjusts the two submitted alignments to agree with the aligned reference by inserting appropriate gaps. See an explanation and example.
Note: this tool may change the order of the reference sequences. Also, all lower case symbols in the sequences will be changed to upper case, all gap characters will be converted to '-', and uneven sequences will be padded with '-' characters to equalize their lengths.