DendroBLAST: Approximate Phylogenetic Trees in the Absence of Multiple Sequence Alignments

New powerful statistics for alignment-free sequence comparison under a pattern transfer model

(2011) Xuemei Liu et al.   JOURNAL OF THEORETICAL BIOLOGY

The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection

(2011) G. Jordan et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives

(2011) Julie D. Thompson et al.   PLoS One

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction

(2010) R. Hagopian et al.   NUCLEIC ACIDS RESEARCH

Quality measures for protein alignment benchmarks

(2010) Robert C. Edgar   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Phylogenetic assessment of alignments reveals neglected tree signal in gaps

(2010) Christophe Dessimoz et al.   GENOME BIOLOGY

Phylogenetic inference under varying proportions of indel-induced alignment gaps

(2009) Bhakti Dwivedi et al.   BMC EVOLUTIONARY BIOLOGY

Alignment-Free Sequence Comparison (I): Statistics and Power

(2009) Gesine Reinert et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2009) K. Liu et al.   SCIENCE

Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space

(2008) Y. Loewenstein et al.   BIOINFORMATICS

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

(2008) Ádám Novák et al.   BIOINFORMATICS

Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?

(2008) Stefanie Hartmann et al.   BMC EVOLUTIONARY BIOLOGY

Evidence for a New Root of the Tree of Life

(2008) James A. Lake et al.   SYSTEMATIC BIOLOGY