TY  - JOUR
A1  - Earl, Dent
A1  - Nguyen, Ngan
A1  - Hickey, Glenn
A1  - Harris, Robert S.
A1  - Fitzgerald, Stephen
A1  - Beal, Kathryn
A1  - Seledtsov, Igor
A1  - Molodtsov, Vladimir
A1  - Raney, Brian J.
A1  - Clawson, Hiram
A1  - Kim, Jaebum
A1  - Kemena, Carsten
A1  - Chang, Jia-Ming
A1  - Erb, Ionas
A1  - Poliakov, Alexander
A1  - Hou, Minmei
A1  - Herrero, Javier
A1  - Kent, William James
A1  - Solovyev, Victor
A1  - Darling, Aaron E.
A1  - Ma, Jian
A1  - Notredame, Cedric
A1  - Brudno, Michael
A1  - Dubchak, Inna
A1  - Haussler, David
A1  - Paten, Benedict
T1  - Alignathon: a competitive assessment of whole-genome alignment methods
Y1  - 2014/12/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 2077 
EP  - 2089 
DO  - 10.1101/gr.174920.114 
VL  - 24 
IS  - 12 
UR  - http://genome.cshlp.org/content/24/12/2077.abstract 
N2  - Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark data sets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem of whole-genome alignment (WGA). Using the same model as the successful Assemblathon competitions, we organized a competitive evaluation in which teams submitted their alignments and then assessments were performed collectively after all the submissions were received. Three data sets were used: Two were simulated and based on primate and mammalian phylogenies, and one was comprised of 20 real fly genomes. In total, 35 submissions were assessed, submitted by 10 teams using 12 different alignment pipelines. We found agreement between independent simulation-based and statistical assessments, indicating that there are substantial accuracy differences between contemporary alignment tools. We saw considerable differences in the alignment quality of differently annotated regions and found that few tools aligned the duplications analyzed. We found that many tools worked well at shorter evolutionary distances, but fewer performed competitively at longer distances. We provide all data sets, submissions, and assessment programs for further study and provide, as a resource for future benchmarking, a convenient repository of code and data for reproducing the simulation assessments. 
ER  -