DACTAL: divide-and-conquer trees (almost) without alignments

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Toward Extracting All Phylogenetic Information from Matrices of Evolutionary Distances

(2010) S. Roch   SCIENCE

The Impact of Multiple Protein Sequence Alignment on Phylogenetic Estimation

(2009) Li-San Wang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

(2009) K. Liu et al.   SCIENCE

StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees

(2008) Ádám Novák et al.   BIOINFORMATICS

Recent developments in the MAFFT multiple sequence alignment program

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