| # | Title | Journal | Year | Citations |
|---|
| 1 | TNT, a free program for phylogenetic analysis | Cladistics | 2008 | 4,493 |
| 2 | TESTING SIGNIFICANCE OF INCONGRUENCE | Cladistics | 1994 | 3,589 |
| 3 | BRANCH SUPPORT AND TREE STABILITY | Cladistics | 1994 | 2,570 |
| 4 | SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information | Cladistics | 2011 | 1,774 |
| 5 | TNT version 1.5, including a full implementation of phylogenetic morphometrics | Cladistics | 2016 | 1,654 |
| 6 | The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis | Cladistics | 1999 | 1,579 |
| 7 | THE RETENTION INDEX AND THE RESCALED CONSISTENCY INDEX | Cladistics | 1989 | 1,561 |
| 8 | PARSIMONY JACKKNIFING OUTPERFORMS NEIGHBOR‐JOINING | Cladistics | 1996 | 1,409 |
| 9 | ESTIMATING CHARACTER WEIGHTS DURING TREE SEARCH | Cladistics | 1993 | 1,035 |
| 10 | CONCEPTS AND TESTS OF HOMOLOGY IN THE CLADISTIC PARADIGM | Cladistics | 1991 | 971 |
| 11 | AMNIOTE PHYLOGENY AND THE IMPORTANCE OF FOSSILS | Cladistics | 1988 | 969 |
| 12 | A review of long-branch attraction | Cladistics | 2005 | 968 |
| 13 | Analyzing Large Data Sets in Reasonable Times: Solutions for Composite Optima | Cladistics | 1999 | 863 |
| 14 | AN AMPLIFICATION OF THE PHYLOGENETIC SPECIES CONCEPT | Cladistics | 1990 | 819 |
| 15 | ON OUTGROUPS | Cladistics | 1993 | 658 |
| 16 | ON SIMULTANEOUS ANALYSIS | Cladistics | 1996 | 605 |
| 17 | Improvements to resampling measures of group support | Cladistics | 2003 | 594 |
| 18 | OPTIMIZATION ALIGNMENT: THE END OF MULTIPLE SEQUENCE ALIGNMENT IN PHYLOGENETICS? | Cladistics | 1996 | 556 |
| 19 | Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification | Cladistics | 2004 | 502 |
| 20 | COULD A CLADOGRAM THIS SHORT HAVE ARISEN BY CHANCE ALONE?: ON PERMUTATION TESTS FOR CLADISTIC STRUCTURE | Cladistics | 1991 | 500 |
| 21 | CLADISTIC TESTS OF ADAPTATIONAL HYPOTHESES | Cladistics | 1988 | 485 |
| 22 | Phylogenetic placement of the Tasmanian spider Acrobleps hygrophilus (Araneae, Anapidae) with comments on the evolution of the capture web in Araneoidea | Cladistics | 2008 | 427 |
| 23 | Choosing Among Multiple Equally Parsimonious Cladograms | Cladistics | 1988 | 419 |
| 24 | The Phylogeny of the Extant Hexapod Orders | Cladistics | 2001 | 417 |
| 25 | THE HOLY GRAIL OF THE PERFECT CHARACTER: THE CLADISTIC TREATMENT OF MORPHOMETRIC DATA | Cladistics | 1993 | 400 |
| 26 | Weighting against homoplasy improves phylogenetic analysis of morphological data sets | Cladistics | 2008 | 386 |
| 27 | CLADISTICS: WHAT'S IN A WORD? | Cladistics | 1993 | 380 |
| 28 | Phylogeny of the Metazoa Based on Morphological and 18S Ribosomal DNA Evidence | Cladistics | 1998 | 360 |
| 29 | SKEWNESS AND PERMUTATION | Cladistics | 1992 | 359 |
| 30 | Logical basis for morphological characters in phylogenetics | Cladistics | 2007 | 354 |
| 31 | The spider tree of life: phylogeny of Araneae based on target‐gene analyses from an extensive taxon sampling | Cladistics | 2017 | 341 |
| 32 | PHYLOGENETIC SYSTEMATICS AND THE SPECIES PROBLEM | Cladistics | 1988 | 336 |
| 33 | Character Coding and Inapplicable Data | Cladistics | 1999 | 326 |
| 34 | Continuous characters analyzed as such | Cladistics | 2006 | 325 |
| 35 | On the inappropriate use of Kimura‐2‐parameter (K2P) divergences in the DNA‐barcoding literature | Cladistics | 2012 | 312 |
| 36 | A comparison of algorithms for the identification of specimens using DNA barcodes: examples from gymnosperms | Cladistics | 2007 | 311 |
| 37 | CONFIDENCE LIMITS ON PHYLOGENIES: THE BOOTSTRAP REVISITED | Cladistics | 1989 | 293 |
| 38 | ARTHROPOD PHYLOGENY: A COMBINED APPROACH | Cladistics | 1993 | 293 |
| 39 | CONSENSUS CLADOGRAMS AND GENERAL CLASSIFICATIONS | Cladistics | 1985 | 289 |
| 40 | Corroboration among Data Sets in Simultaneous Analysis: Hidden Support for Phylogenetic Relationships among Higher Level Artiodactyl Taxa | Cladistics | 1999 | 288 |
| 41 | The Phylogeny of the Extant Chelicerate Orders | Cladistics | 1998 | 287 |
| 42 | RECONSTRUCTING CHARACTER EVOLUTION ON POLYTOMOUS CLADOGRAMS | Cladistics | 1989 | 285 |
| 43 | HEADS AND TAILS: A CHORDATE PHYLOGENY | Cladistics | 1986 | 281 |
| 44 | ON MISSING ENTRIES IN CLADISTIC ANALYSIS | Cladistics | 1991 | 273 |
| 45 | Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology | Cladistics | 2018 | 273 |
| 46 | PARALLEL PHYLOGENIES: RECONSTRUCTING THE HISTORY OF HOST‐PARASITE ASSEMBLAGES | Cladistics | 1994 | 271 |
| 47 | EVOLUTIONARY MORPHOLOGY AND PHYLOGENY OF ARAGHNIDA | Cladistics | 1990 | 268 |
| 48 | Homoplasy Increases Phylogenetic Structure | Cladistics | 1999 | 258 |
| 49 | Methods for Quick Consensus Estimation | Cladistics | 2001 | 250 |
| 50 | THE NATURE OF CLADISTIC DATA | Cladistics | 1987 | 240 |
