Literature

The second edition of Analysis of Phylogenetics and Evolution with R has been published early this year. See HERE for more details.

You may cite this paper if you need a citation for the use of ape:
  • Paradis E., Claude J. & Strimmer K. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289–290. PDF [37 KB]
You can find the list of all references cited in the various help pages of ape HERE.

A list of publications where ape was used for the analyses, cited, or discussed until December 2008 is here. I stopped to maintain this list in early 2009 for the following reasons:
  1. Only a few colleagues sent me references (thanks to them) so I had to find the vast majority of those in the list by myself—a time-consusing hobby.
  2. I wanted the list to be comprehensive and not only to cover the publications indexed in the Web of Knowledge or Scopus, which increased the time spent to find them.
  3. Some journals limit the number of references resulting in ape to be cited in the electronic appendices (e.g., Nature, Science, PNAS), so that though these journals are indexed in the Web of Knowledge, the citation of ape cannot be found this way.
  4. ape is sometimes cited in a way that makes the citation difficult to find.
  5. Some papers do not cite ape though it was obviously used in the analyses because some packages which depend on ape are cited.

The number of citations of ape has increased regularly since 2003.

Below are the counts of the 631 citations of ape in 198 journals between 2003 and 2011.

1: EVOLUTION 45
2: PLOS ONE 33
3: PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON SERIES B BIOLOGICAL SCIENCES 30
4: MOLECULAR PHYLOGENETICS AND EVOLUTION 28
5: JOURNAL OF EVOLUTIONARY BIOLOGY 23
6: MOLECULAR ECOLOGY 21
7: BMC EVOLUTIONARY BIOLOGY 20
8: AMERICAN NATURALIST 17
9: MOLECULAR BIOLOGY AND EVOLUTION 16
10: BIOINFORMATICS 15
11: SYSTEMATIC BIOLOGY 14
12: JOURNAL OF BIOGEOGRAPHY 11
13: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 11
14: BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 10
15: ECOLOGY LETTERS 10
16: NEW PHYTOLOGIST 9
17: ANIMAL BEHAVIOUR 7
18: ECOGRAPHY 7
19: GLOBAL ECOLOGY AND BIOGEOGRAPHY 7
20: OIKOS 7
21: BMC GENOMICS 6
22: FUNCTIONAL ECOLOGY 5
23: NATURE 5
24: OECOLOGIA 5
25: PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B BIOLOGICAL SCIENCES 5
26: BIOLOGY LETTERS 4
27: BMC BIOINFORMATICS 4
28: GLOBAL CHANGE BIOLOGY 4
29: HEREDITY 4
30: JOURNAL OF ANIMAL ECOLOGY 4
31: JOURNAL OF ECOLOGY 4
32: JOURNAL OF THEORETICAL BIOLOGY 4
33: MOLECULAR ECOLOGY RESOURCES 4
34: AMERICAN JOURNAL OF BOTANY 3
35: BRAIN BEHAVIOR AND EVOLUTION 3
36: CONSERVATION BIOLOGY 3
37: DIVERSITY AND DISTRIBUTIONS 3
38: EMERGING INFECTIOUS DISEASES 3
39: EVOLUTIONARY BIOINFORMATICS 3
40: GENOME RESEARCH 3
41: INFECTION GENETICS AND EVOLUTION 3
42: JOURNAL OF AVIAN BIOLOGY 3
43: JOURNAL OF MORPHOLOGY 3
44: MAMMALIAN BIOLOGY 3
45: PALEOBIOLOGY 3
46: PARASITOLOGY 3
47: PHYSIOLOGICAL AND BIOCHEMICAL ZOOLOGY 3
48: PLOS BIOLOGY 3
49: PLOS GENETICS 3
50: PLOS PATHOGENS 3
51: AGRICULTURE ECOSYSTEMS ENVIRONMENT 2
52: APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 2
53: BEHAVIORAL ECOLOGY AND SOCIOBIOLOGY 2
54: BIOLOGICAL CONSERVATION 2
55: CONSERVATION GENETICS 2
56: CORAL REEFS 2
57: DEEP SEA RESEARCH PART II TOPICAL STUDIES IN OCEANOGRAPHY 2
58: ECOLOGICAL ENTOMOLOGY 2
59: ENVIRONMENTAL MICROBIOLOGY 2
60: EVOLUTIONARY BIOLOGY 2
61: EVOLUTIONARY ECOLOGY 2
62: FRONTIERS IN ZOOLOGY 2
63: GENE 2
64: GENETICS 2
65: GENOME 2
66: GENOME BIOLOGY AND EVOLUTION 2
67: INTERNATIONAL JOURNAL FOR PARASITOLOGY 2
68: INTERNATIONAL JOURNAL OF PRIMATOLOGY 2
69: INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 2
70: INVERTEBRATE SYSTEMATICS 2
71: ISME JOURNAL 2
72: JOURNAL OF ANATOMY 2
73: JOURNAL OF MOLECULAR EVOLUTION 2
74: JOURNAL OF VEGETATION SCIENCE 2
75: JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH 2
76: MATHEMATICAL BIOSCIENCES 2
77: METHODS IN ECOLOGY AND EVOLUTION 2
78: PLANT PHYSIOLOGY 2
79: PLANT SYSTEMATICS AND EVOLUTION 2
80: PRESLIA 2
81: STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY 2
82: TAXON 2
83: TRENDS IN ECOLOGY EVOLUTION 2
84: 2007 IEEE SYMPOSIUM ON ARTIFICIAL LIFE 1
85: 2009 INTERNATIONAL CONFERENCE OF SOFT COMPUTING AND PATTERN RECOGNITION 1
86: AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 1
87: AMERICAN JOURNAL OF PRIMATOLOGY 1
88: ANIMAL GENETICS 1
89: ANNALS OF APPLIED STATISTICS 1
90: ARCTIC ANTARCTIC AND ALPINE RESEARCH 1
91: ARDEA 1
92: ATMOSPHERIC ENVIRONMENT 1
93: AUK 1
94: AUSTRAL ECOLOGY 1
95: AUSTRALIAN FORESTRY 1
96: AUSTRALIAN SYSTEMATIC BOTANY 1
97: BEHAVIORAL ECOLOGY 1
98: BEHAVIOUR 1
99: BIOCHEMICAL GENETICS 1
100: BIOLOGICAL REVIEWS 1
101: BIOLOGY DIRECT 1
102: BMC GENETICS 1
103: BMC MEDICAL GENOMICS 1
104: BMC PLANT BIOLOGY 1
105: BOTANICAL JOURNAL OF THE LINNEAN SOCIETY 1
106: BOTANICAL STUDIES 1
107: BRIEFINGS IN BIOINFORMATICS 1
108: BRYOLOGIST 1
109: CANADIAN JOURNAL OF ZOOLOGY REVUE CANADIENNE DE ZOOLOGIE 1
110: CEREBRAL CORTEX 1
111: CHEMOSPHERE 1
112: CLADISTICS 1
113: COGNITIVE LINGUISTICS 1
114: COLD REGIONS SCIENCE AND TECHNOLOGY 1
115: COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A MOLECULAR INTEGRATIVE PHYSIOLOGY 1
116: COMPTES RENDUS PALEVOL 1
117: COMPUTATIONAL SCIENCE ICCS 2009 1
118: COMPUTATIONAL STATISTICS 1
119: COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 1
120: CONSERVATION LETTERS 1
121: CRYPTOGAMIE ALGOLOGIE 1
122: CURRENT BIOLOGY 1
123: CYTOGENETIC AND GENOME RESEARCH 1
124: ECOHEALTH 1
125: ECOLOGICAL APPLICATIONS 1
126: ECOLOGICAL MONOGRAPHS 1
127: ECOLOGICAL RESEARCH 1
128: ECOLOGY 1
129: ELECTRONIC JOURNAL OF COMBINATORICS 1
130: EUROPEAN JOURNAL OF FOREST RESEARCH 1
131: EUROPEAN JOURNAL OF HUMAN GENETICS 1
132: EUROPEAN JOURNAL OF PHYCOLOGY 1
133: FEMS MICROBIOLOGY ECOLOGY 1
134: FLORA 1
135: FOLIA GEOBOTANICA 1
136: FOREST SCIENCE 1
137: GENOME BIOLOGY 1
138: GENOMICS 1
139: HUMAN BIOLOGY 1
140: HYDROBIOLOGIA 1
141: IBIS 1
142: IEEE SYMPOSIUM ON ARTIFICIAL LIFE 1
143: INTELLIGENCE 1
144: JOURNAL OF APPLIED MICROBIOLOGY 1
145: JOURNAL OF BACTERIOLOGY 1
146: JOURNAL OF CLINICAL MICROBIOLOGY 1
147: JOURNAL OF COMPARATIVE PSYCHOLOGY 1
148: JOURNAL OF EXPERIMENTAL BIOLOGY 1
149: JOURNAL OF EXPERIMENTAL ZOOLOGY PART A ECOLOGICAL GENETICS AND PHYSIOLOGY 1
150: JOURNAL OF FIELD ORNITHOLOGY 1
151: JOURNAL OF FISH BIOLOGY 1
152: JOURNAL OF GENERAL VIROLOGY 1
153: JOURNAL OF HYDROLOGY 1
154: JOURNAL OF HYMENOPTERA RESEARCH 1
155: JOURNAL OF INFECTIOUS DISEASES 1
156: JOURNAL OF ORNITHOLOGY 1
157: JOURNAL OF PARASITOLOGY 1
158: JOURNAL OF PERSONALITY AND SOCIAL PSYCHOLOGY 1
159: JOURNAL OF PHYCOLOGY 1
160: JOURNAL OF PLANT ECOLOGY UK 1
161: JOURNAL OF THE NORTH AMERICAN BENTHOLOGICAL SOCIETY 1
162: JOURNAL OF THE ROYAL SOCIETY INTERFACE 1
163: JOURNAL OF VERTEBRATE PALEONTOLOGY 1
164: JOURNAL OF ZOOLOGY 1
165: LANGUAGE 1
166: LECTURE NOTES IN COMPUTER SCIENCE 1
167: LINGUA 1
168: MARINE AND FRESHWATER RESEARCH 1
169: MARINE BIOLOGY 1
170: MARINE MAMMAL SCIENCE 1
171: MEMORIAS DO INSTITUTO OSWALDO CRUZ 1
172: MICROBIAL ECOLOGY 1
173: MOLECULAR MICROBIOLOGY 1
174: MUTATION RESEARCH FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS 1
175: NATURE COMMUNICATIONS 1
176: NATURE GENETICS 1
177: NATURE STRUCTURAL MOLECULAR BIOLOGY 1
178: NEW FORESTS 1
179: ORGANISMS DIVERSITY EVOLUTION 1
180: PALAEONTOLOGIA ELECTRONICA 1
181: PERSPECTIVES IN PLANT ECOLOGY EVOLUTION AND SYSTEMATICS 1
182: PHYTOPATHOLOGY 1
183: PLANT BREEDING 1
184: PLANT DISEASE 1
185: PLANT ECOLOGY 1
186: PLANT ECOLOGY DIVERSITY 1
187: PLANT JOURNAL 1
188: PLOS COMPUTATIONAL BIOLOGY 1
189: PLOS NEGLECTED TROPICAL DISEASES 1
190: PREVENTIVE VETERINARY MEDICINE 1
191: PSYCHOLOGICAL BULLETIN 1
192: SYSTEMATIC BOTANY 1
193: SYSTEMATIC ENTOMOLOGY 1
194: TRENDS IN MICROBIOLOGY 1
195: VISION RESEARCH 1
196: ZOOLOGICA SCRIPTA 1
197: ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 1
198: ZOOSYSTEMA 1

Last updated: March 5, 2012