| MacClade versions 3-4: Analysis of phylogeny and character evolution (1992-2004). DR Maddison, WP Maddison | 10936* | 2004 |
| Mesquite: A modular system for evolutionary analysis WP Maddison, DR Maddison https://www.mesquiteproject.org, 2003 | 9667* | 2003 |
| Gene trees in species trees WP Maddison Systematic biology 46 (3), 523-536, 1997 | 2743 | 1997 |
| Estimation of levels of gene flow from DNA sequence data. RR Hudson, M Slatkin, WP Maddison Genetics 132 (2), 583-589, 1992 | 1599 | 1992 |
| Outgroup analysis and parsimony WP Maddison, MJ Donoghue, DR Maddison Systematic biology 33 (1), 83-103, 1984 | 1371 | 1984 |
| Inferring phylogeny despite incomplete lineage sorting WP Maddison, LL Knowles Systematic biology 55 (1), 21-30, 2006 | 1023 | 2006 |
| Estimating a binary character's effect on speciation and extinction WP Maddison, PE Midford, SP Otto Systematic biology 56 (5), 701-710, 2007 | 878 | 2007 |
| Statistical phylogeography LL Knowles, WP Maddison Molecular Ecology 11 (12), 2623-2635, 2002 | 832 | 2002 |
| A cladistic measure of gene flow inferred from the phylogenies of alleles. M Slatkin, WP Maddison Genetics 123 (3), 603-613, 1989 | 787 | 1989 |
| Reconstructing ancestral character states under Wagner parsimony DL Swofford, WP Maddison Mathematical biosciences 87 (2), 199-229, 1987 | 601 | 1987 |
| NEXUS: an extensible file format for systematic information DR Maddison, DL Swofford, WP Maddison Systematic biology 46 (4), 590-621, 1997 | 581 | 1997 |
| A method for testing the correlated evolution of two binary characters: are gains or losses concentrated on certain branches of a phylogenetic tree? WP Maddison Evolution 44 (3), 539-557, 1990 | 581 | 1990 |
| PDAP package of Mesquite PE Midford, T Garland Jr, WP Maddison Version 1 (1), 2005 | 573* | 2005 |
| Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies RG FitzJohn, WP Maddison, SP Otto Systematic biology 58 (6), 595-611, 2009 | 487 | 2009 |
| Squared-change parsimony reconstructions of ancestral states for continuous-valued characters on a phylogenetic tree WP Maddison Systematic Biology 40 (3), 304-314, 1991 | 474 | 1991 |
| The tree of life web project DR Maddison, KS Schulz, WP Maddison Zootaxa 1668 (1), 19-40, 2007 | 384 | 2007 |
| Missing data versus missing characters in phylogenetic analysis WP Maddison Systematic Biology 42 (4), 576-581, 1993 | 341 | 1993 |
| Reconstructing character evolution on polytomous cladograms W Maddison Cladistics 5 (4), 365-377, 1989 | 311 | 1989 |
| The unsolved challenge to phylogenetic correlation tests for categorical characters WP Maddison, RG FitzJohn Systematic biology 64 (1), 127-136, 2015 | 304 | 2015 |
| Null models for the number of evolutionary steps in a character on a phylogenetic tree WP Maddison, M Slatkin Evolution 45 (5), 1184-1197, 1991 | 288 | 1991 |
David MaddisonProfessor of Zoology, Oregon State UniversityVerified email at science.oregonstate.edu
