MAF (Multiple Alignment Format)

The Multiple Alignment Format stores a series of multiple alignments.   See the UCSC web site for more details.  The extension must be ".maf".  

NOTE: .maf files must be in plain text (not gzipped). The alignment blocks in the file must be sorted by start position, and the file requires an accompanying index. If no index file is detected, IGV will create the index when the file is first loaded, which may result in a delay in loading, depending on the size of the file. Do not close IGV while indexing is in progress.