Iteratively Refined Guide Trees Help Improving Alignment and Phylogenetic Inference in the Mushroom Family Bolbitiaceae

The family Agaricaceae: phylogenies and two new white-spored genera

(2011) Else C. Vellinga et al.   MYCOLOGIA

Galerella nigeriensis (Agaricales), a new species from tropical Africa

(2011) Zdenko Tkalčec et al.   MYCOTAXON

Understanding the Evolutionary Processes of Fungal Fruiting Bodies: Correlated Evolution and Divergence Times in the Psathyrellaceae

(2011) László G. Nagy et al.   SYSTEMATIC BIOLOGY

SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees

(2011) Kevin Liu et al.   SYSTEMATIC BIOLOGY

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

An Alignment Confidence Score Capturing Robustness to Guide Tree Uncertainty

(2010) O. Penn et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolution of autodigestion in the mushroom family Psathyrellaceae (Agaricales) inferred from Maximum Likelihood and Bayesian methods

(2010) László G. Nagy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenetic inference under varying proportions of indel-induced alignment gaps

(2009) Bhakti Dwivedi et al.   BMC EVOLUTIONARY BIOLOGY

Uniting Alignments and Trees

(2009) A. Loytynoja et al.   SCIENCE

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

(2009) K. Liu et al.   SCIENCE

Why Would Phylogeneticists Ignore Computerized Sequence Alignment?

(2009) David A. Morrison   SYSTEMATIC BIOLOGY

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

(2008) Mark P. Simmons et al.   CLADISTICS

jModelTest: Phylogenetic Model Averaging

(2008) D. Posada   MOLECULAR BIOLOGY AND EVOLUTION

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

(2008) A. Loytynoja et al.   SCIENCE