RT Journal
A1 Paten, Benedict
A1 Earl, Dent
A1 Nguyen, Ngan
A1 Diekhans, Mark
A1 Zerbino, Daniel
A1 Haussler, David
T1 Cactus: Algorithms for genome multiple sequence alignment
JF Genome Research 
JO Genome Research 
YR 2011 
FD September 01 
VO 21 
IS 9 
SP 1512 
OP 1528 
DO 10.1101/gr.123356.111 
UL http://genome.cshlp.org/content/21/9/1512.abstract 
AB Much attention has been given to the problem of creating reliable multiple sequence alignments in a model incorporating substitutions, insertions, and deletions. Far less attention has been paid to the problem of optimizing alignments in the presence of more general rearrangement and copy number variation. Using Cactus graphs, recently introduced for representing sequence alignments, we describe two complementary algorithms for creating genomic alignments. We have implemented these algorithms in the new “Cactus” alignment program. We test Cactus using the Evolver genome evolution simulator, a comprehensive new tool for simulation, and show using these and existing simulations that Cactus significantly outperforms all of its peers. Finally, we make an empirical assessment of Cactus's ability to properly align genes and find interesting cases of intra-gene duplication within the primates.