The deterministic effects of alignment bias in phylogenetic inference

Direct optimization overly optimizes data

(2010) KAZUNORI YOSHIZAWA   SYSTEMATIC ENTOMOLOGY

Sandokanid phylogeny based on eight molecular markers—The evolution of a southeast Asian endemic family of Laniatores (Arachnida, Opiliones)

(2009) Prashant Sharma et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Application note: on extension gap in POY version 3

(2008) Andrés Varón et al.   CLADISTICS

Evolution of genomes, host shifts and the geographic spread of SARS-CoV and related coronaviruses

(2008) Daniel Janies et al.   CLADISTICS

The relative sensitivity of different alignment methods and character codings in sensitivity analysis

(2008) Mark P. Simmons et al.   CLADISTICS

The pattern of insertion/deletion polymorphism in Arabidopsis thaliana

(2008) Wen Zhang et al.   MOLECULAR GENETICS AND GENOMICS

A framework for phylogenetic sequence alignment

(2008) David A. Morrison   PLANT SYSTEMATICS AND EVOLUTION

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE

Direct Estimation of the Mitochondrial DNA Mutation Rate in Drosophila melanogaster

(2008) Cathy Haag-Liautard et al.   PLOS BIOLOGY