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1 Introduction

MafFilter is a program for post-processing genome alignments in the Multiple Alignment Files (MAF) format. MAF files consist of a series of "blocks", displaying the alignment of subsequences of the original genomes. In a typical MAF file, such blocks represent synteny blocks. See the UCSC website for a detailed description of the file format.

How to obtain MAF files is not covered in this manual. MAF files are typically generated by packages such as BlastZ, MultiZ, Last or Galaxy, and you should refer to the manual of these resources for more detailed help. These packages also contain tools for manipulating MAF files, which you might find useful in combination to the program described here.

Note that several examples are provided along with the source code of the program, and can serve as good training starts. This manual intends to provide an exhaustive description of the options used in these examples, as well as to provide general information about the way the program works and its underlying algorithms.