FASTSP: linear time calculation of alignment accuracy

PSAR: measuring multiple sequence alignment reliability by probabilistic sampling

(2011) Jaebum Kim et al.   NUCLEIC ACIDS RESEARCH

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

Some remarks on evaluating the quality of the multiple sequence alignment based on the BAliBASE benchmark

(2010) Jacek Błażewicz et al.   International Journal of Applied Mathematics and Computer Science

Issues in bioinformatics benchmarking: the case study of multiple sequence alignment

(2010) M. R. Aniba et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Upcoming challenges for multiple sequence alignment methods in the high-throughput era

(2009) Carsten Kemena et al.   BIOINFORMATICS

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC

(2009) Rahul Satija et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups

(2009) Pablo A. Goloboff et al.   CLADISTICS

Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees

(2009) K. Liu et al.   SCIENCE

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

Alignment Uncertainty and Genomic Analysis

(2008) K. M. Wong et al.   SCIENCE