Indel information eliminates trivial sequence alignment in maximum likelihood phylogenetic analysis

Phylogenetic utility and evolution of indels: A study in neognathous birds

(2011) Łukasz Paśko et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Two Stationary Nonhomogeneous Markov Models of Nucleotide Sequence Evolution

(2010) Vivek Jayaswal et al.   SYSTEMATIC BIOLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

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

POY version 4: phylogenetic analysis using dynamic homologies

(2009) Andrés Varón et al.   CLADISTICS

EXTINCTION RATES SHOULD NOT BE ESTIMATED FROM MOLECULAR PHYLOGENIES

(2009) Daniel L. Rabosky   EVOLUTION

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

(2009) K. Liu et al.   SCIENCE

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

(2008) A. Loytynoja et al.   SCIENCE

Probabilistic Phylogenetic Inference with Insertions and Deletions

(2008) Elena Rivas et al.   PLoS Computational Biology

Incorporation of gap characters and lineage-specific regions into phylogenetic analyses of gene families from divergent clades: an example from the kinesin superfamily across eukaryotes

(2007) Mark P. Simmons et al.   CLADISTICS

Incorporating gaps as phylogenetic characters across eight DNA regions: Ramifications for North American Psoraleeae (Leguminosae)

(2007) Ashley N. Egan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION