SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches

(2009) Stephen A Smith et al.   BMC EVOLUTIONARY BIOLOGY

POY version 4: phylogenetic analysis using dynamic homologies

(2009) Andrés Varón et al.   CLADISTICS

Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy

(2009) K. Liu 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