TY  - JOUR
A1  - Bray, Nicolas
A1  - Pachter, Lior
T1  - MAVID: Constrained Ancestral Alignment of Multiple Sequences
Y1  - 2004/04/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 693 
EP  - 699 
DO  - 10.1101/gr.1960404 
VL  - 14 
IS  - 4 
UR  - http://genome.cshlp.org/content/14/4/693.abstract 
N2  - We describe a new global multiple-alignment program capable of aligning a large number of genomic regions. Our progressive-alignment approach incorporates the following ideas: maximum-likelihood inference of ancestral sequences, automatic guide-tree construction, protein-based anchoring of ab-initio gene predictions, and constraints derived from a global homology map of the sequences. We have implemented these ideas in the MAVID program, which is able to accurately align multiple genomic regions up to megabases long. MAVID is able to effectively align divergent sequences, as well as incomplete unfinished sequences. We demonstrate the capabilities of the program on the benchmark CFTR region, which consists of 1.8 Mb of human sequence and 20 orthologous regions in marsupials, birds, fish, and mammals. Finally, we describe two large MAVID alignments, an alignment of all the available HIV genomes and a multiple alignment of the entire human, mouse, and rat genomes. 
ER  -