maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Optimal Selection of Gene and Ingroup Taxon Sampling for Resolving Phylogenetic Relationships

(2010) Jeffrey P. Townsend et al.   SYSTEMATIC BIOLOGY

Ancestors 1.0: a web server for ancestral sequence reconstruction

(2009) A. B. Diallo et al.   BIOINFORMATICS

primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies

(2009) B. Contreras-Moreira et al.   NUCLEIC ACIDS RESEARCH

UniPrime2: a web service providing easier Universal Primer design

(2009) Robin Boutros et al.   NUCLEIC ACIDS RESEARCH

Genome-wide nucleotide-level mammalian ancestor reconstruction

(2008) B. Paten et al.   GENOME RESEARCH

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions

(2007) E. Torarinsson et al.   GENOME RESEARCH