Why Would Phylogeneticists Ignore Computerized Sequence Alignment?

Correction: An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP)

(2014) Dongying Wu et al.   PLoS One

PRALINETM: a strategy for improved multiple alignment of transmembrane proteins

(2008) W. Pirovano et al.   BIOINFORMATICS

R-Coffee: a method for multiple alignment of non-coding RNA

(2008) A. Wilm et al.   NUCLEIC ACIDS RESEARCH

A framework for phylogenetic sequence alignment

(2008) David A. Morrison   PLANT SYSTEMATICS AND EVOLUTION

Alignment Uncertainty and Genomic Analysis

(2008) K. M. Wong et al.   SCIENCE

The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains

(2008) Pablo Yarza et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Phylogeny Estimation and Alignment via POY versus Clustal + PAUP*: A Response to Ogden and Rosenberg (2007)

(2008) Samuli Lehtonen   SYSTEMATIC BIOLOGY

Uncertainty in homology inferences: Assessing and improving genomic sequence alignment

(2007) G. Lunter et al.   GENOME RESEARCH