| 1 | -- | 2 | Dan Gusfield. Final, Five-Year End, Editorial |
| 3 | -- | 0 | Marie-France Sagot. New EIC Editorial |
| 4 | -- | 6 | Daniel H. Huson, Vincent Moulton, Mike A. Steel. Special Section: Phylogenetics |
| 7 | -- | 21 | Kevin Liu, Serita M. Nelesen, Sindhu Raghavan, C. Randal Linder, Tandy Warnow. Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy |
| 22 | -- | 29 | Bui Quang Minh, Fabio Pardi, Steffen Klaere, Arndt von Haeseler. Budgeted Phylogenetic Diversity on Circular Split Systems |
| 30 | -- | 45 | Simone Linz, Charles Semple. Hybridization in Nonbinary Trees |
| 46 | -- | 61 | Gabriel Cardona, Mercè Llabrés, Francesc Rosselló, Gabriel Valiente. Metrics for Phylogenetic Networks I: Generalizations of the Robinson-Foulds Metric |
| 62 | -- | 75 | Stephen J. Willson. Robustness of Topological Supertree Methods for Reconciling Dense Incompatible Data |
| 76 | -- | 88 | Elizabeth S. Allman, John A. Rhodes. The Identifiability of Covarion Models in Phylogenetics |
| 89 | -- | 95 | Frederick A. Matsen III. Fourier Transform Inequalities for Phylogenetic Trees |
| 96 | -- | 0 | Dan Gusfield. Outgoing EIC Editorial for this Special Section of TCBB with the Theme of Phylogenetics |
| 97 | -- | 102 | Stefan Grünewald, Vincent Moulton. Maximum Parsimony for Tree Mixtures |
| 103 | -- | 109 | Daniel H. Huson. Drawing Rooted Phylogenetic Networks |
| 110 | -- | 117 | Magnus Bordewich, Olivier Gascuel, Katharina T. Huber, Vincent Moulton. Consistency of Topological Moves Based on the Balanced Minimum Evolution Principle of Phylogenetic Inference |
| 118 | -- | 125 | Taoyang Wu, Vincent Moulton, Mike A. Steel. Refining Phylogenetic Trees Given Additional Data: An Algorithm Based on Parsimony |
| 126 | -- | 133 | Elchanan Mossel, Sébastien Roch, Mike A. Steel. Shrinkage Effect in Ancestral Maximum Likelihood |
| 134 | -- | 143 | Jianmin Ma, Minh Ngoc Nguyen 0002, Jagath C. Rajapakse. Gene Classification Using Codon Usage and Support Vector Machines |
| 144 | -- | 157 | Ranjan Maitra. Initializing Partition-Optimization Algorithms |
| 158 | -- | 170 | Sridharakumar Narasimhan, Raghunathan Rengaswamy, Rajanikanth Vadigepalli. Structural Properties of Gene Regulatory Networks: Definitions and Connections |