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JOURNAL

Evolutionary Bioinformatics


An international, peer reviewed, open access journal focusing on evolutionary bioinformatics.  The journal aims to support understanding of organismal form and function through use of molecular, genetic, genomic and proteomic data by giving due consideration to its evolutionary context.

Impact Factor: 1.500 (2016)

Editor in Chief: Dr. Dennis Wall

ISSN: 1176-9343

Processing Speed: High quality, constructive peer review and rapid editorial decision within an average of four weeks.



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2017:13

Phylogenetic Analysis of Nuclear-Encoded RNA Maturases
Sunita Malik, KC Upadhyaya, SM Paul Khurana
Evolutionary Bioinformatics 2017:13 1176934317710945
Original research | Published on 29 May 2017



The Use of Next-Generation Sequencing in the Identification of a Fastidious Pathogen: A Lesson From a Clinical Setup
Amr TM Saeb, Mohamed Abouelhoda, Manojkumar Selvaraju, Sahar I Althawadi, Maysoon Mutabagani, Mohammad Adil, Abdullah Al Hokail, Hamsa T Tayeb
Evolutionary Bioinformatics 2017:13 1176934316686072
Original research | Published on 03 Feb 2017



Corrigendum
Evolutionary Bioinformatics 2017:13 1176934316688670
Original research | Published on 30 Jan 2017



Discovery and Characterisation of Castlerea Virus, a New Species of Isolated in Australia
Caitlin A O’Brien, Breeanna J McLean, Agathe M G Colmant, Jessica J Harrison, Sonja Hall-Mendelin, Andrew F van den Hurk, Cheryl A Johansen, Daniel Watterson, Helle Bielefeldt-Ohmann, Natalee D Newton, Benjamin L Schulz, Roy A Hall, Jody Hobson-Peters
Evolutionary Bioinformatics 2017:13 1176934317691269
Original research | Published on 23 Feb 2017



The Transposon Provides Messages That Yield Unique Profiles of Protein Isoforms and Acts Synergistically With to Enrich Proteome Complexity via Exonization
Yuh-Chyang Charng, Lung-Hsin Hsu, Li-yu Daisy Liu
Evolutionary Bioinformatics 2017:13 1176934317690410
Original research | Published on 23 Feb 2017



Numericware i: Identical by State Matrix Calculator
Bongsong Kim, William D Beavis
Evolutionary Bioinformatics 2017:13 1176934316688663
Original research | Published on 10 Mar 2017



Simulation-Based Evaluation of Hybridization Network Reconstruction Methods in the Presence of Incomplete Lineage Sorting
Olga K Kamneva, Noah A Rosenberg
Evolutionary Bioinformatics 2017:13 1176934317691935
Original research | Published on 10 Mar 2017



A Method to Categorize 2-Dimensional Patterns Using Statistics of Spatial Organization
Juan López-Sauceda, Mara D Rueda-Contreras
Evolutionary Bioinformatics 2017:13 1176934317697978
Original research | Published on 10 Mar 2017



A New Hybrid MGBPSO-GSA Variant for Improving Function Optimization Solution in Search Space
Narinder Singh, Sharandeep Singh, S B Singh
Evolutionary Bioinformatics 2017:13 1176934317699855
Original research | Published on 22 Mar 2017



Free-Living Enterobacterium 24613: Complete Genome Sequence and Metabolic Profiling
Kateřina Snopková, Karel Sedlář, Juraj Bosák, Eva Chaloupková, Ivo Sedláček, Ivo Provazník, David Šmajs
Evolutionary Bioinformatics 2017:13 1176934317700863
Original research | Published on 30 Mar 2017



Performance of Hidden Markov Models in Recovering the Standard Classification of Glycoside Hydrolases
Mariana Fonseca Rossi, Beatriz Mello, Carlos G Schrago
Evolutionary Bioinformatics 2017:13 1176934317703401
Original research | Published on 20 Apr 2017



Conservation of Repeats at the Mammalian KCNQ1OT1-CDKN1C Region Suggests a Role in Genomic Imprinting
Marcos De Donato, Tanveer Hussain, Hectorina Rodulfo, Sunday O Peters, Ikhide G Imumorin, Bolaji N Thomas
Evolutionary Bioinformatics 2017:13 1176934317715238
Original research | Published on 16 Jun 2017



RapaNet: A Web Tool for the Co-Expression Analysis of Genes
Jiye Kim, Kyong Mi Jun, Joung Sug Kim, Songhwa Chae, Yoon-Mok Pahk, Tae-Ho Lee, Soo-In Sohn, Soo In Lee, Myung-Ho Lim, Chang-Kug Kim, Yoonkang Hur, Baek Hie Nahm, Yeon-Ki Kim
Evolutionary Bioinformatics 2017:13 1176934317715421
Original research | Published on 19 Jun 2017



Genome-Wide Identification and Comparative Analysis of Albumin Family in Vertebrates
Shugang Li, Yiping Cao, Fang Geng
Evolutionary Bioinformatics 2017:13 1176934317716089
Original research | Published on 19 Jun 2017



2016:12

pATsi: Paralogs and Singleton Genes from Arabidopsis thaliana
Luca Ambrosino, Hamed Bostan, Pasquale di Salle, Mara Sangiovanni, Alessandra Vigilante, and Maria L. Chiusano
Evolutionary Bioinformatics 2016:12 1-7
Original research | Published on 11 Jan 2016



Genome-Wide Analysis of NBS-LRR Genes in Sorghum Genome Revealed Several Events Contributing to NBS-LRR Gene Evolution in Grass Species
Xiping Yang and Jianping Wang
Evolutionary Bioinformatics 2016:12 9-21
Original research | Published on 14 Jan 2016



A Polyglot Approach to Bioinformatics Data Integration: A Phylogenetic Analysis of HIV-1
Steven Reisman, Thomas Hatzopoulos, Konstantin Läufer, George K. Thiruvathukal, and Catherine Putonti
Evolutionary Bioinformatics 2016:12 23-27
Original research | Published on 18 Jan 2016



Structural Diversity of a Novel LTR Retrotransposon, RTPOSON, in the Genus Oryza
Yu-Chia Hsu, Chang-Sheng Wang, Yann-Rong Lin and Yong-Pei Wu
Evolutionary Bioinformatics 2016:12 29-40
Original research | Published on 18 Jan 2016



Genome Sequence and Analysis of Peptoclostridium difficile Strain ZJCDC-S82
Yun Luo, Chen Huang, Julian Ye, Weijia Fang, Wanjun Gu, Zhiping Chen, Hui Li, XianJun Wang and Dazhi Jin
Evolutionary Bioinformatics 2016:12 41-49
Original research | Published on 24 Jan 2016



NABIC: A New Access Portal to Search, Visualize, and Share Agricultural Genomics Data
Young-Joo Seol, Tae-Ho Lee, Dong-Suk Park and Chang-Kug Kim
Evolutionary Bioinformatics 2016:12 51-58
Original research | Published on 01 Feb 2016



Phi Class of Glutathione S-transferase Gene Superfamily Widely Exists in Nonplant Taxonomic Groups
Jean-Pierre Munyampundu, You-Ping Xu and Xin-Zhong Cai
Evolutionary Bioinformatics 2016:12 59-71
Original research | Published on 10 Feb 2016



HTSFinder: Powerful Pipeline of DNA Signature Discovery by Parallel and Distributed Computing
Ramin Karimi and Andras Hajdu
Evolutionary Bioinformatics 2016:12 73-85
Original research | Published on 10 Feb 2016



Estimating Divergence Times and Substitution Rates in Rhizobia
Rim Chriki-Adeeb and Ali Chriki
Evolutionary Bioinformatics 2016:12 87-97
Original research | Published on 03 May 2016



Diversity and Evolution of Disease Resistance Genes in Barley (Hordeum vulgare L.)
Ethan J. Andersen, Shaukat Ali, R. Neil Reese, Yang Yen, Surendra Neupane and Madhav P. Nepal
Evolutionary Bioinformatics 2016:12 99-108
Original research | Published on 04 May 2016



Phylogenetic and Structural Analysis of Polyketide Synthases in Aspergilli
Preetida J. Bhetariya, Madhvi Prajapati, Asani Bhaduri, Rahul Shubhra Mandal, Anupam Varma, Taruna Madan, Yogendra Singh and P. Usha Sarma
Evolutionary Bioinformatics 2016:12 109-119
Original research | Published on 10 May 2016



Coevolution of RAC Small GTPases and their Regulators GEF Proteins
Alejandro Jiménez-Sánchez
Evolutionary Bioinformatics 2016:12 121-131
Original research | Published on 17 May 2016



The Simple Chordate Ciona intestinalis Has a Reduced Complement of Genes Associated with Fanconi Anemia
Edward C. Stanley, Paul A. Azzinaro, David A. Vierra, Niall G. Howlett and Steven Q. Irvine
Evolutionary Bioinformatics 2016:12 133-148
Original research | Published on 06 Jun 2016



Partitional Classification: A Complement to Phylogeny
Marc Salomon and Bruno Dassy
Evolutionary Bioinformatics 2016:12 149-156
Original research | Published on 16 Jun 2016



Investigating Evolutionary Dynamics of RHA1 Operons
Yong Chen, Dandan Geng, Kristina Ehrhardt and Shaoqiang Zhang
Evolutionary Bioinformatics 2016:12 157-163
Original research | Published on 28 Jun 2016



Notes on the Statistical Power of the Binary State Speciation and Extinction (BiSSE) Model
Alexander Gamisch
Evolutionary Bioinformatics 2016:12 165-174
Original research | Published on 26 Jul 2016



Comparative Transcriptome Analysis Reveals Substantial Tissue Specificity in Human Aortic Valve
Jun Wang, Ying Wang, Weidong Gu, Buqing Ni, Haoliang Sun, Tong Yu, Wanjun Gu, Liang Chen and Yongfeng Shao
Evolutionary Bioinformatics 2016:12 175-184
Original research | Published on 31 Jul 2016



Molecular Evolution of the Yersinia Major Outer Membrane Protein C (OmpC)
Anna M. Stenkova, Evgeniya P. Bystritskaya, Konstantin V. Guzev, Alexander V. Rakin and Marina P. Isaeva
Evolutionary Bioinformatics 2016:12 185-191
Original research | Published on 21 Aug 2016



MultiSyn: A Webtool for Multiple Synteny Detection and Visualization of User’s Sequence of Interest Compared to Public Plant Species
Jeong-Ho Baek, Junah Kim, Chang-Kug Kim, Seong-Han Sohn, Dongsu Choi, Milind B. Ratnaparkhe, Do-Wan Kim and Tae-Ho Lee
Evolutionary Bioinformatics 2016:12 193-199
Original research | Published on 28 Aug 2016



Revisiting Myosin Families Through Large-scale Sequence Searches Leads to the Discovery of New Myosins
Shaik Naseer Pasha, Iyer Meenakshi and Ramanathan Sowdhamini
Evolutionary Bioinformatics 2016:12 201-211
Original research | Published on 29 Aug 2016



Genomics Study of Mycobacterium tuberculosis Strains from Different Ethnic Populations in Taiwan
Horng-Yunn Dou, Yih-Yuan Chen, Ying-Tsong Chen, Jia-Ru Chang, Chien-Hsing Lin, Keh-Ming Wu, Ming-Shian Lin, Ih-Jen Su and Shih-Feng Tsai
Evolutionary Bioinformatics 2016:12 213-221
Original research | Published on 27 Sep 2016



Approaching Long Genomic Regions and Large Recombination Rates with msParSm as an Alternative to MaCS
Carlos Montemuiño, Antonio Espinosa, Juan C. Moure, Gonzalo Vera, Porfidio Hernández and Sebastián Ramos-Onsins
Evolutionary Bioinformatics 2016:12 223-228
Original research | Published on 02 Oct 2016



A Novel Method for Alignment-free DNA Sequence Similarity Analysis Based on the Characterization of Complex Networks
Jie Zhou, Pianyu Zhong and Tinghui Zhang
Evolutionary Bioinformatics 2016:12 229-235
Original research | Published on 06 Oct 2016



IBBOMSA: An Improved Biogeography-based Approach for Multiple Sequence Alignment
Rohit Kumar Yadav and Haider Banka
Evolutionary Bioinformatics 2016:12 237-246
Original research | Published on 27 Oct 2016



A Bioinformatics Approach for Detecting Repetitive Nested Motifs using Pattern Matching
José R. Romero, Jessica A. Carballido, Ingrid Garbus, Viviana C. Echenique and Ignacio Ponzoni
Evolutionary Bioinformatics 2016:12 247-251
Original research | Published on 30 Oct 2016



A Multilayered Screening Method for the Identification of Regulatory Genes in Rice by Agronomic Traits
Young-Joo Seol, So Youn Won, Younhee Shin, Jong-Yeol Lee, Jong-Sik Chun, Yong-Kab Kim and Chang-Kug Kim
Evolutionary Bioinformatics 2016:12 253-262
Original research | Published on 02 Nov 2016



A Comparative In Silico Study of the Antioxidant Defense Gene Repertoire of Distinct Lifestyle Trypanosomatid Species
Ingrid Thaís Beltrame-Botelho, Carlos Talavera-López, Björn Andersson, Edmundo Carlos Grisard and Patricia Hermes Stoco
Evolutionary Bioinformatics 2016:12 263-275
Original research | Published on 07 Nov 2016



EvalMSA: A Program to Evaluate Multiple Sequence Alignments and Detect Outliers
Alvaro Chiner-Oms and Fernando González-Candelas
Evolutionary Bioinformatics 2016:12 277-284
Original research | Published on 28 Nov 2016



Support Vector Machines Trained with Evolutionary Algorithms Employing Kernel Adatron for Large Scale Classification of Protein Structures
Nancy Arana-Daniel, Alberto A. Gallegos, Carlos López-Franco, Alma Y. Alanís, Jacob Morales and Adriana López-Franco
Evolutionary Bioinformatics 2016:12 285-302
Original research | Published on 04 Dec 2016



Current Bacterial Gene Encoding Capsule Biosynthesis Protein CapI Contains Nucleotides Derived from Exonization
Yong Wang, Xia-Fang Tao, Zhi-Xi Su, A-Ke Liu, Tian-Lei Liu, Ling Sun, Qin Yao, Ke-Ping Chen and Xun Gu
Evolutionary Bioinformatics 2016:12 303-312
Original research | Published on 12 Dec 2016



Prefiltering Model for Homology Detection Algorithms on GPU
Germán Retamosa, Luis de Pedro, Ivan González and Javier Tamames
Evolutionary Bioinformatics 2016:12 313-322
Original research | Published on 18 Dec 2016



2016:Suppl. 1 Bioinformatics Methods and Applications for Big Metagenomics Data

Genome Sequencing and Evolutionary Analysis of Marine Gut Fungus Aspergillus sp. Z5 from Ligia oceanica
Xue Li, Jin-Zhong Xu, Wen-Jie Wang, Yi-Wang Chen, Dao-Qiong Zheng, Ya-Nan Di, Ping Li, Pin-Mei Wang and Yu-Dong Li
Evolutionary Bioinformatics 2016:Suppl. 1 1-4
Original research | Published on 03 Apr 2016



Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis
Vanessa Aguiar-Pulido, Wenrui Huang, Victoria Suarez-Ulloa, Trevor Cickovski, Kalai Mathee and Giri Narasimhan
Evolutionary Bioinformatics 2016:Suppl. 1 5-16
Original research | Published on 12 May 2016



Bipartite Graphs for Visualization Analysis of Microbiome Data
Karel Sedlar, Petra Videnska, Helena Skutkova, Ivan Rychlik and Ivo Provaznik
Evolutionary Bioinformatics 2016:Suppl. 1 17-23
Original research | Published on 31 May 2016



Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges
Katherine Bruder, Kema Malki, Alexandria Cooper, Emily Sible, Jason W. Shapiro, Siobhan C. Watkins and Catherine Putonti
Evolutionary Bioinformatics 2016:Suppl. 1 25-33
Original research | Published on 20 Jun 2016



2016:Suppl. 2 Evolution of the insect virome

Bioinformatic Characterization of Mosquito Viromes within the Eastern United States and Puerto Rico: Discovery of Novel Viruses
Kenneth G. Frey, Tara Biser, Theron Hamilton, Carlos J. Santos, Guillermo Pimentel, Vishwesh P. Mokashi and Kimberly A. Bishop-Lilly
Evolutionary Bioinformatics 2016:Suppl. 2 1-12
Original research | Published on 16 Jun 2016



Twenty-Five New Viruses Associated with the Drosophilidae (Diptera)
Claire L. Webster, Ben Longdon, Samuel H. Lewis, and Darren J. Obbard
Evolutionary Bioinformatics 2016:Suppl. 2 13-25
Original research | Published on 20 Jun 2016



Archival Collections are Important in the Study of the Biology, Diversity, and Evolution of Arboviruses
Alyssa T. Pyke and David Warrilow
Evolutionary Bioinformatics 2016:Suppl. 2 27-30
Original research | Published on 14 Sep 2016



Virus Discovery Using Tick Cell Lines
Lesley Bell-Sakyi and Houssam Attoui
Evolutionary Bioinformatics 2016:Suppl. 2 31-34
Original research | Published on 15 Sep 2016



Commensal Viruses of Mosquitoes: Host Restriction, Transmission, and Interaction with Arboviral Pathogens
Roy A. Hall, Helle Bielefeldt-Ohmann, Breeanna J. McLean, Caitlin A. O'Brien, Agathe M.G. Colmant, Thisun B.H. Piyasena, Jessica J. Harrison, Natalee D. Newton, Ross T. Barnard, Natalie A. Prow, Joshua M. Deerain, Marcus G.K.Y. Mah, and Jody Hobson-Peters
Evolutionary Bioinformatics 2016:Suppl. 2 35-44
Original research | Published on 10 Jan 2017



2015:11

Correction to: “In Silico Detection of Virulence Gene Homologues in the Human Pathogen Sphingomonas Spp.”
Amr TM Saeb, Satish Kumar David and Hissa Al-Brahim
Evolutionary Bioinformatics 2015:11 1-1
Original research | Published on 14 Jan 2015



Classification of Metagenomics Data at Lower Taxonomic Level Using a Robust Supervised Classifier
Tao Hou, Fu Liu, Yun Liu, Qing Yu Zou, Xiao Zhang and Ke Wang
Evolutionary Bioinformatics 2015:11 3-10
Original research | Published on 26 Jan 2015



windex: Analyzing Convergent Evolution Using the Wheatsheaf Index in R
Kevin Arbuckle and Amanda Minter
Evolutionary Bioinformatics 2015:11 11-14
Original research | Published on 12 Feb 2015



A Novel Approach to Identify Candidate Prognostic Factors for Hepatitis C Treatment Response Integrating Clinical and Viral Genetic Data
Alicia Amadoz and Fernando González-Candelas
Evolutionary Bioinformatics 2015:11 15-24
Original research | Published on 23 Feb 2015



Extensive Genomic Variability of Knops Blood Group Polymorphisms Is Associated with Sickle Cell Disease in Africa
Kimberley C. Duru, Jenelle A. Noble, Aldiouma Guindo, Li Yi, Ikhide G. Imumorin, Dapa A. Diallo and Bolaji N. Thomas
Evolutionary Bioinformatics 2015:11 25-33
Original research | Published on 09 Mar 2015



IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments
Muhammad Tariq Pervez, Masroor Ellahi Babar, Asif Nadeem, Naeem Aslam, Nasir Naveed, Sarfraz Ahmad, Shah Muhammad, Salman Qadri, Muhammad Shahid, Tanveer Hussain and Maryam Javed
Evolutionary Bioinformatics 2015:11 35-42
Original research | Published on 12 Mar 2015



A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway
Mark A. Miller, Terri Schwartz, Brett E. Pickett, Sherry He, Edward B. Klem, Richard H. Scheuermann, Maria Passarotti, Seth Kaufman and Maureen A. O’Leary
Evolutionary Bioinformatics 2015:11 43-48
Original research | Published on 16 Mar 2015



CNL Disease Resistance Genes in Soybean and Their Evolutionary Divergence
Madhav P. Nepal and Benjamin V. Benson
Evolutionary Bioinformatics 2015:11 49-63
Original research | Published on 07 Apr 2015



Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity
Yueying Qi, Wenjing Xu, Tian Xing, Mingming Zhao, Nana Li, Li Yan, Guangmin Xia and Mengcheng Wang
Evolutionary Bioinformatics 2015:11 65-77
Original research | Published on 07 Apr 2015



BIR Pipeline for Preparation of Phylogenomic Data
Surendra Kumar, Anders K. Krabberød, Ralf S. Neumann, Katerina Michalickova, Sen Zhao, Xiaoli Zhang and Kamran Shalchian-Tabrizi
Evolutionary Bioinformatics 2015:11 79-83
Original research | Published on 27 Apr 2015



Roles of Solvent Accessibility and Gene Expression in Modeling Protein Sequence Evolution
Kuangyu Wang, Shuhui Yu, Xiang Ji, Clemens Lakner, Alexander Griffing and Jeffrey L. Thorne
Evolutionary Bioinformatics 2015:11 85-96
Original research | Published on 29 Apr 2015



TRUFA: A User-Friendly Web Server for de novo RNA-seq Analysis Using Cluster Computing
Etienne Kornobis, Luis Cabellos, Fernando Aguilar, Cristina Frías-López, Julio Rozas, Jesús Marco and Rafael Zardoya
Evolutionary Bioinformatics 2015:11 97-104
Original research | Published on 24 May 2015



Molecular Evolutionary Analysis of β-Defensin Peptides in Vertebrates
Jianbo Tu, Diyan Li, Qingqing Li, Long Zhang, Qing Zhu, Uma Gaur, Xiaolan Fan, Huailiang Xu, Yongfang Yao, Xiaoling Zhao and Mingyao Yang
Evolutionary Bioinformatics 2015:11 105-114
Original research | Published on 01 Jun 2015



MITOSCISSOR: A Useful Tool for Auto-Assembly of Mitogenomic Datasets in the Evolutionary Analysis of Fishes
Zheng Sun, Yuanzhi Cheng and Junbin Zhang
Evolutionary Bioinformatics 2015:11 115-120
Original research | Published on 14 Jun 2015



MSL: A Measure to Evaluate Three-dimensional Patterns in Gene Expression Data
David Gutiérrez-Avilés and Cristina Rubio-Escudero
Evolutionary Bioinformatics 2015:11 121-135
Original research | Published on 23 Jun 2015



The Origin of Land Plants: A Phylogenomic Perspective
Bojian Zhong, Linhua Sun and David Penny
Evolutionary Bioinformatics 2015:11 137-141
Original research | Published on 08 Jul 2015



Effective Population Size and Signatures of Selection Using Bovine 50K SNP Chips in Korean Native Cattle (Hanwoo)
Yi Li and Jong-Joo Kim
Evolutionary Bioinformatics 2015:11 143-153
Original research | Published on 08 Jul 2015



Using Nonlinear Stochastic Evolutionary Game Strategy to Model an Evolutionary Biological Network of Organ Carcinogenesis Under a Natural Selection Scheme
Bor-Sen Chen, Kun-Wei Tsai and Cheng-Wei Li
Evolutionary Bioinformatics 2015:11 155-178
Original research | Published on 19 Jul 2015



A Visualization Tool for Calculating the Genetic Substitution Patterns Between Two Different Groups
Insung Ahn, Jin-Hwa Jang, Ha-Yeon Kim, Ji-Hae Lee, and Hyeon Seok Son
Evolutionary Bioinformatics 2015:11 179-183
Original research | Published on 27 Jul 2015



How Many Genes are Needed to Resolve Phylogenetic Incongruence?
Bin Ai and Ming Kang
Evolutionary Bioinformatics 2015:11 185-188
Original research | Published on 10 Aug 2015



In Silico Characterization of Functional Divergence of Two Cathelicidin Variants in Indian Sheep
Kamaljeet K. Dhaliwal, Jaspreet S. Arora, Chandra S. Mukhopadhyay and Prem P. Dubey
Evolutionary Bioinformatics 2015:11 189-196
Original research | Published on 01 Sep 2015



Genomics and Evolution in Traditional Medicinal Plants: Road to a Healthier Life
Da-Cheng Hao and Pei-Gen Xiao
Evolutionary Bioinformatics 2015:11 197-212
Original research | Published on 04 Oct 2015



Phylogenetic Trees and Networks Reduce to Phylogenies on Binary States: Does It Furnish an Explanation to the Robustness of Phylogenetic Trees against Lateral Transfers?
Marc Thuillard and Didier Fraix-Burnet
Evolutionary Bioinformatics 2015:11 213-221
Original research | Published on 13 Oct 2015



Soft Computing Methods for Disulfide Connectivity Prediction
Alfonso E. Márquez-Chamorro and Jesús S. Aguilar-Ruiz
Evolutionary Bioinformatics 2015:11 223-229
Original research | Published on 20 Oct 2015



In Silico Gene Regulatory Network of the Maurer’s Cleft Pathway in Plasmodium falciparum
Itunuoluwa Isewon, Jelili Oyelade, Benedikt Brors and Ezekiel Adebiyi
Evolutionary Bioinformatics 2015:11 231-238
Original research | Published on 22 Oct 2015



Screening of Transcription Factors Involved in Fetal Hemoglobin Regulation Using Phylogenetic Footprinting
Gisele Cristine de Souza Carrocini, Larissa Paola Rodrigues Venancio and Claudia Regina Bonini-Domingos
Evolutionary Bioinformatics 2015:11 239-244
Original research | Published on 27 Oct 2015



Using Disease-Associated Coding Sequence Variation to Investigate Functional Compensation by Human Paralogous Proteins
Sayaka Miura, Stephanie Tate and Sudhir Kumar
Evolutionary Bioinformatics 2015:11 245-251
Original research | Published on 02 Nov 2015



Segmenting the Human Genome into Isochores
Paolo Cozzi, Luciano Milanesi and Giorgio Bernardi
Evolutionary Bioinformatics 2015:11 253-261
Original research | Published on 25 Nov 2015



SUMAC: Constructing Phylogenetic Supermatrices and Assessing Partially Decisive Taxon Coverage
William A. Freyman
Evolutionary Bioinformatics 2015:11 263-266
Original research | Published on 30 Nov 2015



Why do Sequence Signatures Predict Enzyme Mechanism? Homology versus Chemistry
Kirsten E. Beattie, Luna De Ferrari and John B. O. Mitchell
Evolutionary Bioinformatics 2015:11 267-274
Original research | Published on 29 Dec 2015



2015:Suppl. 1 RNA: An Expanding View of Function and Evolution

Genome-Wide Characterization of miRNAs Involved in N Gene-Mediated Immunity in Response to Tobacco Mosaic Virus in Nicotiana benthamiana
Kangquan Yin, Yang Tang and Jinping Zhao
Evolutionary Bioinformatics 2015:Suppl. 1 1-11
Original research | Published on 07 Jan 2015



Apparent microRNA-Target-specific Histone Modification in Mammalian Spermatogenesis
Y-H Taguchi
Evolutionary Bioinformatics 2015:Suppl. 1 13-26
Original research | Published on 24 Feb 2015



RNA-seq Reveals Complicated Transcriptomic Responses to Drought Stress in a Nonmodel Tropic Plant, Bombax ceiba L.
Zhili Zhou, Huancheng Ma, Kevin Lin, Youjie Zhao, Yuan Chen, Zhi Xiong, Liuyang Wang and Bin Tian
Evolutionary Bioinformatics 2015:Suppl. 1 27-37
Original research | Published on 23 Jun 2015



De Novo Transcriptome Assembly and Development of Novel Microsatellite Markers for the Traditional Chinese Medicinal Herb, Veratrilla baillonii Franch (Gentianaceae)
Lei Wang, Zhengkun Wang, Jianbing Chen, Chunyan Liu, Wanlong Zhu, Liuyang Wang and Lihua Meng
Evolutionary Bioinformatics 2015:Suppl. 1 39-45
Original research | Published on 08 Jul 2015



Genome-wide Identification of WRKY Genes in the Desert Poplar Populus euphratica and Adaptive Evolution of the Genes in Response to Salt Stress
Jianchao Ma, Jing Lu, Jianmei Xu, Bingbing Duan, Xiaodong He and Jianquan Liu
Evolutionary Bioinformatics 2015:Suppl. 1 47-55
Original research | Published on 05 Aug 2015



Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster
Dahai Gao, Dennis C. Ko, Xinmin Tian, Guang Yang and Liuyang Wang
Evolutionary Bioinformatics 2015:Suppl. 1 57-65
Original research | Published on 13 Sep 2015



Discovering All Transcriptome Single-Nucleotide Polymorphisms and Scanning for Selection Signatures in Ducks (Anas platyrhynchos)
Ruiyi Lin, Xiaoyong Du, Sixue Peng, Liubin Yang, Yunlong Ma, Yanzhang Gong and Shijun Li
Evolutionary Bioinformatics 2015:Suppl. 1 67-76
Original research | Published on 01 Dec 2015



Introductory Editorial: RNA: An Expanding View of Function and Evolution
Xinwei Han, Yuan Chen, Liuyang Wang, Wenwen Fang, Ning Zhang, Qiyun Zhu
Evolutionary Bioinformatics 2015:Suppl. 1 77-79
Original research | Published on 14 Jan 2016



Phylotranscriptomic Analysis Based on Coalescence was Less Influenced by the Evolving Rates and the Number of Genes: A Case Study in Ericales
Lu Zhang, Wei Wu, Hai-Fei Yan and Xue-Jun Ge
Evolutionary Bioinformatics 2015:Suppl. 1 81-91
Original research | Published on 18 Jan 2016



2015:Suppl. 2 Evolutionary Genomics

Phylogeny Inference of Closely Related Bacterial Genomes: Combining the Features of Both Overlapping Genes and Collinear Genomic Regions
Yan-Cong Zhang and Kui Lin
Evolutionary Bioinformatics 2015:Suppl. 2 1-9
Original research | Published on 17 Dec 2015



Gene Tree Affects Inference of Sites Under Selection by the Branch-Site Test of Positive Selection
Yoan Diekmann and José B. Pereira-Leal
Evolutionary Bioinformatics 2015:Suppl. 2 11-17
Original research | Published on 18 Jan 2016



Using UNIFORMAT and GENE[RATE] to Analyze Data with Ambiguities in Population Genetics
José Manuel Nunes
Evolutionary Bioinformatics 2015:Suppl. 2 19-26
Original research | Published on 21 Feb 2016



Forward-in-Time, Spatially Explicit Modeling Software to Simulate Genetic Lineages Under Selection
Mathias Currat, Pascale Gerbault, Da Di, José M. Nunes and Alicia Sanchez-Mazas
Evolutionary Bioinformatics 2015:Suppl. 2 27-39
Original research | Published on 25 Feb 2016



Surprisingly Low Limits of Selection in Plant Domestication
Robin G. Allaby, James L. Kitchen and Dorian Q. Fuller
Evolutionary Bioinformatics 2015:Suppl. 2 41-51
Original research | Published on 05 Apr 2016



Introductory Editorial: Evolutionary Genomics
Yuval Itan, Gur Pines and Pascale Gerbault
Evolutionary Bioinformatics 2015:Suppl. 2 53-55
Original research | Published on 20 Apr 2016



Human Dispersal Out of Africa: A Lasting Debate
Saioa López, Lucy van Dorp and Garrett Hellenthal
Evolutionary Bioinformatics 2015:Suppl. 2 57-68
Original research | Published on 21 Apr 2016



Correction to: “Forward-in-Time, Spatially Explicit Modeling Software to Simulate Genetic Lineages Under Selection”
Mathias Currat, Pascale Gerbault, Da Di, José M. Nunes and Alicia Sanchez-Mazas
Evolutionary Bioinformatics 2015:Suppl. 2 69-69
Original research | Published on 29 May 2016



Comparative Genomics of Amphibian-like Ranaviruses, Nucleocytoplasmic Large DNA Viruses of Poikilotherms
Stephen J. Price
Evolutionary Bioinformatics 2015:Suppl. 2 71-82
Original research | Published on 25 Oct 2016



2014:10

Netmes: Assessing Gene Network Inference Algorithms by Network-Based Measures
Gökmen Altay, Zeyneb Kurt, Matthias Dehmer and Frank Emmert-Streib
Evolutionary Bioinformatics 2014:10 1-9
Original research | Published on 06 Feb 2014



RapidMic: Rapid Computation of the Maximal Information Coefficient
Dongming Tang, Mingwen Wang, Weifan Zheng and Hongjun Wang
Evolutionary Bioinformatics 2014:10 11-16
Original research | Published on 06 Feb 2014



The Stochastic Evolutionary Game for a Population of Biological Networks Under Natural Selection
Bor-Sen Chen and Shih-Ju Ho
Evolutionary Bioinformatics 2014:10 17-38
Original research | Published on 16 Feb 2014



Phylogenetic Relationships of Some Filamentous Cyanoprokaryotic Species
Plamen Stoyanov, Dzhemal Moten, Rumen Mladenov, Balik Dzhambazov and Ivanka Teneva
Evolutionary Bioinformatics 2014:10 39-49
Original research | Published on 23 Feb 2014



TreSpEx—Detection of Misleading Signal in Phylogenetic Reconstructions Based on Tree Information
Torsten H. Struck
Evolutionary Bioinformatics 2014:10 51-67
Original research | Published on 31 Mar 2014



A Multistep Screening Method to Identify Genes Using Evolutionary Transcriptome of Plants
Chang-Kug Kim, Hye-Min Lim, Jong-Kuk Na, Ji-Weon Choi, Seong-Han Sohn, Soo-Chul Park, Young-Hwan Kim, Yong-Kab Kim and Dool-Yi Kim
Evolutionary Bioinformatics 2014:10 69-78
Original research | Published on 21 Apr 2014



Assignment of Calibration Information to Deeper Phylogenetic Nodes is More Effective in Obtaining Precise and Accurate Divergence Time Estimates
Beatriz Mello and Carlos G. Schrago
Evolutionary Bioinformatics 2014:10 79-85
Original research | Published on 07 May 2014



Similarity/Dissimilarity Analysis of Protein Sequences Based on a New Spectrum-Like Graphical Representation
Yuhua Yao, Shoujiang Yan, Huimin Xu, Jianning Han, Xuying Nan, Ping-an He and Qi Dai
Evolutionary Bioinformatics 2014:10 87-96
Original research | Published on 12 Jun 2014



Influence of Modularity and Regularity on Disparity of Atelostomata Sea Urchins
Juan López-Sauceda, Juan Malda-Barrera, Alfredo Laguarda-Figueras, Francisco Solís-Marín and José L. Aragón
Evolutionary Bioinformatics 2014:10 97-105
Original research | Published on 29 Jun 2014



Regulation of Human PAX6 Expression by miR-7
Maria Needhamsen, Robert B. White, Keith M. Giles, Sarah A. Dunlop and Meghan G. Thomas
Evolutionary Bioinformatics 2014:10 107-113
Original research | Published on 14 Jul 2014



An In-depth Analysis of a Multilocus Phylogeny Identifies leuS As a Reliable Phylogenetic Marker for the Genus Pantoea
James T. Tambong, Renlin Xu, Cynthia-Anne Kaneza and Jean-Claude Nshogozabahizi
Evolutionary Bioinformatics 2014:10 115-125
Original research | Published on 27 Jul 2014



iteRates: An R Package for Implementing a Parametric Rate Comparison on Phylogenetic Trees
James A. Fordyce, Premal Shah and Benjamin M. Fitzpatrick
Evolutionary Bioinformatics 2014:10 127-130
Original research | Published on 03 Aug 2014



The Comparative Genomics and Phylogenomics of Leishmania amazonensis Parasite
Diogo A Tschoeke, Gisele L Nunes, Rodrigo Jardim, Joana Lima, Aline SR Dumaresq, Monete R Gomes, Leandro de Mattos Pereira, Daniel R Loureiro, Patricia H Stoco, Herbert Leonel de Matos Guedes, Antonio Basilio de Miranda, Jeronimo Ruiz, André Pitaluga, Floriano P Silva Jr, Christian M Probst, Nicholas J Dickens, Jeremy C Mottram, Edmundo C Grisard and Alberto MR Dávila
Evolutionary Bioinformatics 2014:10 131-153
Original research | Published on 23 Sep 2014



A New Method for Motif Mining in Biological Networks
Yuan Xu, Qiang Zhang and Changjun Zhou
Evolutionary Bioinformatics 2014:10 155-163
Original research | Published on 01 Oct 2014



Comparative Study on Sequence–Structure–Function Relationship of the Human Short-chain Dehydrogenases/Reductases Protein Family
Nu Thi Ngoc Tang and Ly Le
Evolutionary Bioinformatics 2014:10 165-176
Original research | Published on 21 Oct 2014



Cloning and Expression Profiling of the Polycomb Gene, Retinoblastoma-related Protein from Tomato Solanum lycopersicum L.
Zainab M. Almutairi and Monther T. Sadder
Evolutionary Bioinformatics 2014:10 177-185
Original research | Published on 23 Oct 2014



Evolutionary Analysis and Prediction of Peptide Vaccine Candidates for Foot-and-Mouth-Disease Virus Types A and O in Bangladesh
Samina Momtaz, Arafat Rahman, Munawar Sultana and M. Anwar Hossain
Evolutionary Bioinformatics 2014:10 187-196
Original research | Published on 03 Nov 2014



SWAMP: Sliding Window Alignment Masker for PAML
Peter W. Harrison, Gregory E. Jordan and Stephen H. Montgomery
Evolutionary Bioinformatics 2014:10 197-204
Original research | Published on 01 Dec 2014



Evaluating the Accuracy and Efficiency of Multiple Sequence Alignment Methods
Muhammad Tariq Pervez, Masroor Ellahi Babar, Asif Nadeem, Muhammad Aslam, Ali Raza Awan, Naeem Aslam, Tanveer Hussain, Nasir Naveed, Salman Qadri, Usman Waheed and Muhammad Shoaib
Evolutionary Bioinformatics 2014:10 205-217
Original research | Published on 07 Dec 2014



Functional Implications of RNA Splicing for Human Long Intergenic Noncoding RNAs
Feng-Chi Chen, Chia-Lin Pan and Hsuan-Yu Lin
Evolutionary Bioinformatics 2014:10 219-228
Original research | Published on 10 Dec 2014



In Silico Detection of Virulence Gene Homologues in the Human Pathogen Sphingomonas Spp.
Amr T. M. Saeb, Satish Kumar David and Hissa Al-Brahim
Evolutionary Bioinformatics 2014:10 229-238
Original research | Published on 11 Dec 2014



Computational Analysis Reveals a Successive Adaptation of Multiple Inositol Polyphosphate Phosphatase 1 in Higher Organisms Through Evolution
Surya P. Kilaparty, Awantika Singh, William H. Baltosser and Nawab Ali
Evolutionary Bioinformatics 2014:10 239-250
Original research | Published on 22 Dec 2014



2013:9

The Molecular Evolutionary Patterns of the Insulin/FOXO Signaling Pathway
Minghui Wang, Qishan Wang, Zhen Wang, Qingping Wang, Xiangzhe Zhang and Yuchun Pan
Evolutionary Bioinformatics 2013:9 1-16
Original research | Published on 10 Jan 2013



TIRfinder: A Web Tool for Mining Class II Transposons Carrying Terminal Inverted Repeats
Tomasz Gambin, Michał Startek, Krzysztof Walczak, Jarosław Paszek, Dariusz Grzebelus and Anna Gambin
Evolutionary Bioinformatics 2013:9 17-27
Original research | Published on 22 Jan 2013



A Proximity-Based Method to Identify Genomic Regions Correlated with a Continuously Varying Environmental Variable
Cornelia Di Gaetano, Giuseppe Matullo, Alberto Piazza, Moreno Ursino and Mauro Gasparini
Evolutionary Bioinformatics 2013:9 29-42
Original research | Published on 29 Jan 2013



A Unifying Mathematical Framework for Genetic Robustness, Environmental Robustness, Network Robustness and their Trade-off on Phenotype Robustness in Biological Networks Part I: Gene Regulatory Networks in Systems and Evolutionary Biology
Bor-Sen Chen and Ying-Po Lin
Evolutionary Bioinformatics 2013:9 43-68
Original research | Published on 26 Feb 2013



A Unifying Mathematical Framework for Genetic Robustness, Environmental Robustness, Network Robustness and their Tradeoff on Phenotype Robustness in Biological Networks Part II: Ecological Networks
Bor-Sen Chen and Ying-Po Lin
Evolutionary Bioinformatics 2013:9 69-85
Original research | Published on 26 Feb 2013



A Unifying Mathematical Framework for Genetic Robustness, Environmental Robustness, Network Robustness and their Trade-offs on Phenotype Robustness in Biological Networks. Part III: Synthetic Gene Networks in Synthetic Biology
Bor-Sen Chen and Ying-Po Lin
Evolutionary Bioinformatics 2013:9 87-109
Original research | Published on 26 Feb 2013



CMCpy: Genetic Code-Message Coevolution Models in Python
Peter J. Becich, Brian P. Stark, Harish S. Bhat and David H. Ardell
Evolutionary Bioinformatics 2013:9 111-125
Original research | Published on 27 Feb 2013



EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes
Tanja Magoc, Derrick Wood and Steven L. Salzberg,
Evolutionary Bioinformatics 2013:9 127-136
Original research | Published on 10 Mar 2013



Design of Synthetic Genetic Oscillators Using Evolutionary Optimization
Yen-Chang Chang, Chun-Liang Lin and Tanagorn Jennawasin
Evolutionary Bioinformatics 2013:9 137-150
Original research | Published on 10 Mar 2013



Circulation of Human Respiratory Syncytial Virus Strains Among Hospitalized Children with Acute Lower Respiratory Infection in Malaysia
Mohammad Reza Etemadi, Zamberi Sekawi, Norlijah Othman, Munn-Sann Lye and Faezeh Yazdani Moghaddam
Evolutionary Bioinformatics 2013:9 151-161
Original research | Published on 10 Apr 2013



A Tool Preference Choice Method for RNA Secondary Structure Prediction by SVM with Statistical Tests
Chiou-Yi Hor, Chang-Biau Yang, Chia-Hung Chang, Chiou-Ting Tseng and Hung-Hsin Chen
Evolutionary Bioinformatics 2013:9 163-184
Original research | Published on 14 Apr 2013



Top-Down Clustering for Protein Subfamily Identification
Eduardo P. Costa, Celine Vens and Hendrik Blockeel
Evolutionary Bioinformatics 2013:9 185-202
Original research | Published on 06 May 2013



Antiviral Stratagems Against HIV-1 Using RNA Interference (RNAi) Technology
Dimitrios Vlachakis, Georgia Tsiliki, Athanasia Pavlopoulou, Maria G. Roubelakis, Spyridon Champeris Tsaniras and Sophia Kossida
Evolutionary Bioinformatics 2013:9 203-213
Original research | Published on 16 May 2013



Analysis of Synonymous Codon Usage Patterns in Seven Different Citrus Species
Chen Xu, Jing Dong, Chunfa Tong, Xindong Gong, Qiang Wen and Qiang Zhuge
Evolutionary Bioinformatics 2013:9 215-228
Original research | Published on 23 May 2013



Comment on “The Molecular Evolutionary Patterns of the Insulin/FOXO Signaling Pathway”
David Alvarez-Ponce, Montserrat Aguadé and Julio Rozas
Evolutionary Bioinformatics 2013:9 229-234
Original research | Published on 10 Jun 2013



rbrothers: R Package for Bayesian Multiple Change-Point Recombination Detection
Jan Irvahn, Sujay Chattopadhyay, Evgeni V. Sokurenko and Vladimir N. Minin
Evolutionary Bioinformatics 2013:9 235-238
Original research | Published on 12 Jun 2013



Molecular Evolution and Functional Divergence of Soluble Starch Synthase Genes in Cassava (Manihot Esculenta Crantz)
Zefeng Yang, Yifan Wang, Shuhui Xu, Chenwu Xu and Changjie Yan
Evolutionary Bioinformatics 2013:9 239-249
Original research | Published on 03 Jul 2013



Effective Encoding for DNA Sequence Visualization Based on Nucleotide’s Ring Structure
A.T.M. Golam Bari, Mst. Rokeya Reaz, A.K.M. Tauhidul Islam, Ho-Jin Choi and Byeong-Soo Jeong
Evolutionary Bioinformatics 2013:9 251-261
Original research | Published on 07 Jul 2013



SARP: A Novel Algorithm to Assess Compositional Biases in Protein Sequences
Kirill S. Antonets and Anton A. Nizhnikov
Evolutionary Bioinformatics 2013:9 263-273
Original research | Published on 11 Jul 2013



Conserved Nonsense-Prone CpG Sites in Apoptosis-Regulatory Genes: Conditional Stop Signs on the Road to Cell Death
Yongzhong Zhao and Richard J. Epstein
Evolutionary Bioinformatics 2013:9 275-283
Original research | Published on 14 Jul 2013



Identification of Differentially Evolved Genes: An Alternative Approach to Detection of Accelerated Molecular Evolution from Genome-Wide Comparative Data
Kyu-Won Kim, David W. Burt, Heebal Kim and Seoae Cho
Evolutionary Bioinformatics 2013:9 285-299
Original research | Published on 28 Jul 2013



Evolutionary Modeling of Genotype-Phenotype Associations, and Application to Primate Coding and Non-coding mtDNA Rate Variation
Timothy D. O'Connor and Nicholas I. Mundy
Evolutionary Bioinformatics 2013:9 301-316
Original research | Published on 28 Jul 2013



Conventional Simulation of Biological Sequences Leads to a Biased Assessment of Multi-Loci Phylogenetic Analysis
Barbara O. Aguiar and Carlos G. Schrago
Evolutionary Bioinformatics 2013:9 317-325
Original research | Published on 13 Aug 2013



Analysis of Protein Thermostability Enhancing Factors in Industrially Important Thermus Bacteria Species
Benjamin Kumwenda, Derek Litthauer, Özlem Tastan Bishop, and Oleg Reva
Evolutionary Bioinformatics 2013:9 327-342
Original research | Published on 18 Aug 2013



POPBAM: Tools for Evolutionary Analysis of Short Read Sequence Alignments
Daniel Garrigan
Evolutionary Bioinformatics 2013:9 343-353
Original research | Published on 01 Sep 2013



SBEToolbox: A Matlab Toolbox for Biological Network Analysis
Kranti Konganti, Gang Wang, Ence Yang and James J. Cai
Evolutionary Bioinformatics 2013:9 355-362
Original research | Published on 01 Sep 2013



Identification, Nomenclature, and Evolutionary Relationships of Mitogen-Activated Protein Kinase (MAPK) Genes in Soybean
Achal Neupane, Madhav P. Nepal, Sarbottam Piya, Senthil Subramanian, Jai S. Rohila, R. Neil Reese and Benjamin V. Benson
Evolutionary Bioinformatics 2013:9 363-386
Original research | Published on 22 Sep 2013



Prediction of Protein Essentiality by the Support Vector Machine with Statistical Tests
Chiou-Yi Hor, Chang-Biau Yang, Zih-Jie Yang and Chiou-Ting Tseng
Evolutionary Bioinformatics 2013:9 387-416
Original research | Published on 03 Oct 2013



Analysis of New Functional Profiles of Protein Isoforms Yielded by Ds Exonization in Rice
Ting-Ying Chien, Li-yu Daisy Liu, and Yuh-Chyang Charng
Evolutionary Bioinformatics 2013:9 417-427
Original research | Published on 09 Oct 2013 | Video Abstract Available



PhyloTreePruner: A Phylogenetic Tree-Based Approach for Selection of Orthologous Sequences for Phylogenomics
Kevin M. Kocot, Mathew R. Citarella, Leonid L. Moroz and Kenneth M. Halanych
Evolutionary Bioinformatics 2013:9 429-435
Original research | Published on 29 Oct 2013



Identification of New Aquaporin Genes and Single Nucleotide Polymorphism in Bread Wheat
B. Pandey, P. Sharma, D.M. Pandey, I. Sharma and R. Chatrath
Evolutionary Bioinformatics 2013:9 437-452
Original research | Published on 03 Nov 2013



The Origin of Parasitism Gene in Nematodes: Evolutionary Analysis Through the Construction of Domain Trees
Yizi Yang and Damin Luo
Evolutionary Bioinformatics 2013:9 453-466
Original research | Published on 06 Nov 2013



Grouped False-Discovery Rate for Removing the Gene-Set-Level Bias of RNA-seq
Tae Young Yang and Seongmun Jeong
Evolutionary Bioinformatics 2013:9 467-478
Original research | Published on 13 Nov 2013



Computational Identification of MicroRNAs from the Expressed Sequence Tags of Toxic Dinofiagellate Alexandrium Tamarense
Dahai Gao, Limei Qiu, Zhanhui Hou, Qingchun Zhang, Jianmin Wu, Qiang Gao and Linsheng Song
Evolutionary Bioinformatics 2013:9 479-485
Original research | Published on 20 Nov 2013



EASER: Ensembl Easy Sequence Retriever
Emanuel Maldonado, Imran Khan, Siby Philip, Vítor Vasconcelos and Agostinho Antunes
Evolutionary Bioinformatics 2013:9 487-490
Original research | Published on 24 Nov 2013



A Comprehensive Phylogenetic Analysis of Deadenylases
Athanasia Pavlopoulou, Dimitrios Vlachakis, Nikolaos A.A. Balatsos and Sophia Kossida
Evolutionary Bioinformatics 2013:9 491-497
Original research | Published on 02 Dec 2013



Approximate Likelihood Estimation of Divergence Time Range Using a Coalescent-based Model
Arindam RoyChoudhury
Evolutionary Bioinformatics 2013:9 499-509
Original research | Published on 10 Dec 2013



2012:8

Species Delimitation and Global Biosecurity
Laura M. Boykin, Karen F. Armstrong, Laura Kubatko and Paul De Barro
Evolutionary Bioinformatics 2012:8 1-37
Original research | Published on 08 Dec 2011 | Video Abstract Available



LCGbase: A Comprehensive Database for Lineage-Based Co-regulated Genes
Dapeng Wang, Yubin Zhang, Zhonghua Fan, Guiming Liu and Jun Yu
Evolutionary Bioinformatics 2012:8 39-46
Original research | Published on 13 Dec 2011



SAFE Software and FED Database to Uncover Protein-Protein Interactions using Gene Fusion Analysis
Dimosthenis Tsagrasoulis, Vasilis Danos,, Maria Kissa, Philip Trimpalis, V. Lila Koumandou, Amalia D. Karagouni, Athanasios Tsakalidis and Sophia Kossida
Evolutionary Bioinformatics 2012:8 47-60
Original research | Published on 18 Dec 2011



EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data
Benjamin Linard, Ngoc Hoan Nguyen, Francisco Prosdocimi, Olivier Poch and Julie D. Thompson
Evolutionary Bioinformatics 2012:8 61-77
Original research | Published on 21 Dec 2011



BS-KNN: An Effective Algorithm for Predicting Protein Subchloroplast Localization
Jing Hu and Xianghe Yan
Evolutionary Bioinformatics 2012:8 79-87
Original research | Published on 05 Jan 2012



Evolutionary Genomics of Genes Involved in Olfactory Behavior in the Drosophila melanogaster Species Group
Nicolás Lavagnino, François Serra, Leonardo Arbiza, Hernán Dopazo and Esteban Hasson,
Evolutionary Bioinformatics 2012:8 89-104
Original research | Published on 09 Jan 2012



Interkingdom Gene Transfer May Contribute to the Evolution of Phytopathogenicity in Botrytis Cinerea
Bo Zhu, Qing Zhou, Guanlin Xie, Guoqing Zhang, Xiaowei Zhang, Yanli Wang, Gunchang Sun, Bin Li and Gulei Jin
Evolutionary Bioinformatics 2012:8 105-117
Original research | Published on 11 Jan 2012



Construction of a Pig Physical Interactome Using Sequence Homology and a Comprehensive Reference Human Interactome
Felix Dreher, Atanas Kamburov and Ralf Herwig
Evolutionary Bioinformatics 2012:8 119-126
Original research | Published on 24 Jan 2012



Testing Synchrony in Historical Biogeography: The Case of New World Primates and Hystricognathi Rodents
Leticia Loss-Oliveira, Barbara O. Aguiar and Carlos G. Schrago*
Evolutionary Bioinformatics 2012:8 127-137
Original research | Published on 24 Jan 2012



Inferring the Phylogeny of Bovidae Using Mitochondrial DNA Sequences: Resolving Power of Individual Genes Relative to Complete Genomes
Ibrahim A. Arif, Mohammad A. Bakir and Haseeb A. Khan
Evolutionary Bioinformatics 2012:8 139-150
Original research | Published on 20 Feb 2012



easyPAC: A Tool for Fast Prediction, Testing and Reference Mapping of Degenerate PCR Primers from Alignments or Consensus Sequences
David Rosenkranz
Evolutionary Bioinformatics 2012:8 151-159
Original research | Published on 14 Mar 2012 | Video Abstract Available



Selection of Marker Genes Using Whole-Genome DNA Polymorphism Analysis
Harry M. Bohle and Toni Gabaldón
Evolutionary Bioinformatics 2012:8 161-169
Original research | Published on 19 Mar 2012



A Lossy Compression Technique Enabling Duplication-Aware Sequence Alignment
Valerio Freschi and Alessandro Bogliolo
Evolutionary Bioinformatics 2012:8 171-180
Original research | Published on 02 Apr 2012



Promoter Sequences Prediction Using Relational Association Rule Mining
Gabriela Czibula, Maria-Iuliana Bocicor and Istvan Gergely Czibula
Evolutionary Bioinformatics 2012:8 181-196
Original research | Published on 23 Apr 2012



Efficient Feature Selection and Multiclass Classification with Integrated Instance and Model Based Learning
Zhenqiu Liu, Halima Bensmail and Ming Tan
Evolutionary Bioinformatics 2012:8 197-205
Original research | Published on 30 Apr 2012



Impact of the Partitioning Scheme on Divergence Times Inferred from Mammalian Genomic Data Sets
Carolina M. Voloch and Carlos G. Schrago
Evolutionary Bioinformatics 2012:8 207-218
Original research | Published on 14 May 2012



Mitochondrial Genetic Differentiation of Spirlin (Actinopterigii: Cyprinidae) in the South Caspian Sea basin of Iran
Mahvash Seifali, Aziz Arshad, Faezeh Yazdani Moghaddam, Hamid Reza Esmaeili, Bahram H. Kiabi, Siti Khalijah Daud and Mansour Aliabadian
Evolutionary Bioinformatics 2012:8 219-227
Original research | Published on 21 May 2012



Cross-Genome Clustering of Human and C. elegans G-Protein Coupled Receptors
Balasubramanian Nagarathnam, Singaravelu Kalaimathy, Veluchamy Balakrishnan and Ramanathan Sowdhamini
Evolutionary Bioinformatics 2012:8 229-259
Original research | Published on 19 Jun 2012



PhyloTempo: A Set of R Scripts for Assessing and Visualizing Temporal Clustering in Genealogies Inferred from Serially Sampled Viral Sequences
Melissa M. Norström, Mattia C.F. Prosperi, Rebecca R. Gray, Annika C. Karlsson and Marco Salemi
Evolutionary Bioinformatics 2012:8 261-269
Original research | Published on 11 Jun 2012



Evolution of the RALF Gene Family in Plants: Gene Duplication and Selection Patterns
Jun Cao, and Feng Shi
Evolutionary Bioinformatics 2012:8 271-292
Original research | Published on 11 Jun 2012



MiIP: The Monomer Identification and Isolation Program
Christopher Bun, William Ziccardi, Jeffrey Doering and Catherine Putonti
Evolutionary Bioinformatics 2012:8 293-300
Original research | Published on 14 Jun 2012



Transposon-Derived and Satellite-Derived Repetitive Sequences Play Distinct Functional Roles in Mammalian Intron Size Expansion
Dapeng Wang, Yao Su, Xumin Wang, Hongxing Lei and Jun Yu
Evolutionary Bioinformatics 2012:8 301-319
Original research | Published on 19 Jun 2012



AP2/ERF Transcription Factor in Rice: Genome-Wide Canvas and Syntenic Relationships between Monocots and Eudicots
Muhammad Rashid, He Guangyuan, Yang Guangxiao, Javeed Hussain and Yan Xu
Evolutionary Bioinformatics 2012:8 321-355
Original research | Published on 21 Jun 2012



RY-Coding and Non-Homogeneous Models Can Ameliorate the Maximum-Likelihood Inferences From Nucleotide Sequence Data with Parallel Compositional Heterogeneity
Sohta A. Ishikawa, Yuji Inagaki, and Tetsuo Hashimoto
Evolutionary Bioinformatics 2012:8 357-371
Original research | Published on 25 Jun 2012



Phylogenomic and Domain Analysis of Iterative Polyketide Synthases in Aspergillus Species
Shu-Hsi Lin, Miwa Yoshimoto, Ping-Chiang Lyu, Chuan-Yi Tang and Masanori Arita
Evolutionary Bioinformatics 2012:8 373-387
Original research | Published on 04 Jul 2012



Determinants of Exon-Level Evolutionary Rates in Arabidopsis Species
Gideon C.-T. Wu, and Feng-Chi Chen
Evolutionary Bioinformatics 2012:8 389-415
Original research | Published on 04 Jul 2012



Reliable Phylogenetic Trees Building: A New Web Interface for FIGENIX
Julien Paganini and Philippe Gouret
Evolutionary Bioinformatics 2012:8 417-421
Original research | Published on 05 Jul 2012



PhyloMarker—A Tool for Mining Phylogenetic Markers Through Genome Comparison: Application of the Mouse Lemur (Genus Microcebus) Phylogeny
Runhua Lei, Thaine W. Rowley, Lifeng Zhu, Carolyn A. Bailey, Shannon E. Engberg, Mindy L. Wood, Mary C. Christman, George H. Perry, Edward E. Louis Jr and Guoqing Lu
Evolutionary Bioinformatics 2012:8 423-435
Original research | Published on 23 Jul 2012



The Chordate Proteome History Database
Anthony Levasseur, Julien Paganini, Jacques Dainat, Julie D. Thompson, Olivier Poch, Pierre Pontarotti and Philippe Gouret
Evolutionary Bioinformatics 2012:8 437-447
Original research | Published on 01 Aug 2012



Inference of Self-Regulated Transcriptional Networks by Comparative Genomics
Joseph P. Cornish, Fialelei Matthews, Julien R. Thomas and Ivan Erill
Evolutionary Bioinformatics 2012:8 449-461
Original research | Published on 06 Aug 2012



Efficiency of Nuclear and Mitochondrial Markers Recovering and Supporting Known Amniote Groups
Julia Lambret-Frotté, Fernando Araújo Perini and Claudia Augusta de Moraes Russo
Evolutionary Bioinformatics 2012:8 463-473
Original research | Published on 06 Aug 2012



TreeCmp: Comparison of Trees in Polynomial Time
Damian Bogdanowicz, Krzysztof Giaro and Borys Wróbel,
Evolutionary Bioinformatics 2012:8 475-487
Original research | Published on 06 Aug 2012



Meta-Analysis of General Bacterial Subclades in Whole-Genome Phylogenies Using Tree Topology Profiling
Thomas Meinel and Antje Krause
Evolutionary Bioinformatics 2012:8 489-525
Original research | Published on 07 Aug 2012



Cloud Computing for Comparative Genomics with Windows Azure Platform
Insik Kim, Jae-Yoon Jung, Todd F. DeLuca, Tristan H. Nelson and Dennis P. Wall
Evolutionary Bioinformatics 2012:8 527-534
Original research | Published on 30 Aug 2012



Evolution of Type II Antifreeze Protein Genes in Teleost Fish: A Complex Scenario Involving Lateral Gene Transfers and Episodic Directional Selection
Ulf Sorhannus
Evolutionary Bioinformatics 2012:8 535-544
Original research | Published on 17 Sep 2012



Phylogenomic Study of Lipid Genes Involved in Microalgal Biofuel Production—Candidate Gene Mining and Metabolic Pathway Analyses
Namrata Misra, Prasanna Kumar Panda, Bikram Kumar Parida and Barada Kanta Mishra
Evolutionary Bioinformatics 2012:8 545-564
Original research | Published on 20 Sep 2012



Translation Efficiency in Upstream Region of microRNA Targets in Arabidopsis thaliana
Wanjun Gu, Chuanying Zhai, Xiaofei Wang, Xueying Xie, Gurunadh Parinandi, and Tong Zhou,
Evolutionary Bioinformatics 2012:8 565-574
Original research | Published on 25 Sep 2012



Genome-Wide Survey of Ds Exonization to Enrich Transcriptomes and Proteomes in Plants
Li-yu Daisy Liu and Yuh-Chyang Charng
Evolutionary Bioinformatics 2012:8 575-587
Original research | Published on 08 Oct 2012 | Video Abstract Available



Phylogenetic Analysis and Comparative Genomics of Purine Riboswitch Distribution in Prokaryotes
Payal Singh and Supratim Sengupta
Evolutionary Bioinformatics 2012:8 589-609
Original research | Published on 06 Nov 2012



A Novel Multi-Scale Modeling Approach to Infer Whole Genome Divergence
Eli Reuveni and Alessandro Giuliani
Evolutionary Bioinformatics 2012:8 611-622
Original research | Published on 14 Nov 2012



Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus
Ence Yang, Amanda M. Hulse and James J. Cai
Evolutionary Bioinformatics 2012:8 623-644
Original research | Published on 19 Nov 2012



2011:7

SOLiDzipper: A High Speed Encoding Method for the Next-Generation Sequencing Data
Young Jun Jeon, Sang Hyun Park, Sung Min Ahn and Hee Joung Hwang
Evolutionary Bioinformatics 2011:7 1-6
Original research | Published on 10 Mar 2011



Phylogenetic Analysis of Kindlins Suggests Subfunctionalization of an Ancestral Unduplicated Kindlin into Three Paralogs in Vertebrates
Ammad Aslam Khan, Axel Janke, Takashi Shimokawa and Hongquan Zhang
Evolutionary Bioinformatics 2011:7 7-19
Original research | Published on 22 Mar 2011



FORS-D Analysis in P. falciparum can Differentiate Classes of Genes Under Selection
Atish Kathpal, Balakota Reddy Patakottu and Swati Patankar
Evolutionary Bioinformatics 2011:7 21-29
Original research | Published on 20 Mar 2011



A Monte Carlo Method for Assessing the Quality of Duplication-Aware Alignment Algorithms
Valerio Freschi and Alessandro Bogliolo
Evolutionary Bioinformatics 2011:7 31-40
Original research | Published on 10 May 2011



Evolutionary Implications and Physicochemical Analyses of Selected Proteins of Type III Polyketide Synthase Family
V. Mallika, K.C. Sivakumar and E.V. Soniya
Evolutionary Bioinformatics 2011:7 41-53
Original research | Published on 29 May 2011



Structurama: Bayesian Inference of Population Structure
John P. Huelsenbeck, Peter Andolfatto and Edna T. Huelsenbeck
Evolutionary Bioinformatics 2011:7 55-59
Original research | Published on 02 Jun 2011



How Fitch-Margoliash Algorithm can Benefit from Multi Dimensional Scaling
Sylvain Lespinats, Delphine Grando, Eric Maréchal, Mohamed-Ali Hakimi, Olivier Tenaillon and Olivier Bastien
Evolutionary Bioinformatics 2011:7 61-85
Original research | Published on 07 Jun 2011



Functional Evolution of BRCT Domains from Binding DNA to Protein
Zi-Zhang Sheng, Yu-Qi Zhao, and Jing-Fei Huang
Evolutionary Bioinformatics 2011:7 87-97
Original research | Published on 12 Jun 2011



Three-Dimensional Structure of Arabidopsis thaliana Lipase Predicted by Homology Modeling Method
Abdelmonaem Messaoudi, Hatem Belguith and Jeannette Ben Hamida
Evolutionary Bioinformatics 2011:7 99-105
Original research | Published on 28 Jun 2011



Phylogenomics-Based Reconstruction of Protozoan Species Tree
Kary A.C.S. Ocaña, and Alberto M.R. Dávila
Evolutionary Bioinformatics 2011:7 107-121
Original research | Published on 31 Jul 2011



IONS: Identification of Orthologs by Neighborhood and Similarity—an Automated Method to Identify Orthologs in Chromosomal Regions of Common Evolutionary Ancestry and its Application to Hemiascomycetous Yeasts
Marie-Line Seret and Philippe V. Baret
Evolutionary Bioinformatics 2011:7 123-133
Original research | Published on 30 Aug 2011



Single-Domain Parvulins Constitute a Specific Marker for Recently Proposed Deep-Branching Archaeal Subgroups
Christoph Lederer, Dominik Heider, Johannes van den Boom, Daniel Hoffmann, Jonathan W. Mueller and Peter Bayer
Evolutionary Bioinformatics 2011:7 135-148
Original research | Published on 19 Sep 2011



A Novel Model for DNA Sequence Similarity Analysis Based on Graph Theory
Xingqin Qi, Qin Wu, Yusen Zhang, Eddie Fuller and Cun-Quan Zhang
Evolutionary Bioinformatics 2011:7 149-158
Original research | Published on 04 Oct 2011



A New Support Measure to Quantify the Impact of Local Optima in Phylogenetic Analyses
Grant Brammer, Seung-Jin Sul and Tiffani L. Williams
Evolutionary Bioinformatics 2011:7 159-170
Original research | Published on 29 Sep 2011



Profiles and Majority Voting-Based Ensemble Method for Protein Secondary Structure Prediction
Hafida Bouziane, Belhadri Messabih and Abdallah Chouarfia
Evolutionary Bioinformatics 2011:7 171-189
Original research | Published on 10 Oct 2011



Characterization and Inference of Gene Gain/Loss Along Burkholderia Evolutionary History
Bo Zhu, Shengli Zhou, Miaomiao Lou, Jun Zhu, Bin Li, Guanlin Xie, GuLei Jin, and René De Mot
Evolutionary Bioinformatics 2011:7 191-200
Original research | Published on 18 Oct 2011



On the Interplay between the Evolvability and Network Robustness in an Evolutionary Biological Network: A Systems Biology Approach
Bor-Sen Chen and Ying-Po Lin
Evolutionary Bioinformatics 2011:7 201-233
Original research | Published on 01 Nov 2011



In Silico Prediction of Evolutionarily Conserved GC-Rich Elements Associated with Antigenic Proteins of Plasmodium falciparum
Porkodi Panneerselvam, Praveen Bawankar, Surashree Kulkarni, and Swati Patankar
Evolutionary Bioinformatics 2011:7 235-255
Original research | Published on 10 Nov 2011



ColorPhylo: A Color Code to Accurately Display Taxonomic Classifications
Sylvain Lespinats and Bernard Fertil
Evolutionary Bioinformatics 2011:7 257-270
Original research | Published on 13 Nov 2011



Factors Affecting Synonymous Codon Usage Bias in Chloroplast Genome of Oncidium Gower Ramsey
Chen Xu, Xiaoning Cai, Quanzhan Chen, Hongxia Zhou, Yao Cai and Ailing Ben
Evolutionary Bioinformatics 2011:7 271-278
Original research | Published on 14 Nov 2011



Evolution of Antifreeze Protein Genes in the Diatom Genus Fragilariopsis: Evidence for Horizontal Gene Transfer, Gene Duplication and Episodic Diversifying Selection
Ulf Sorhannus
Evolutionary Bioinformatics 2011:7 279-289
Original research | Published on 15 Nov 2011



2010:6

Comparative Molecular Evolution of Trichoderma Chitinases in Response to Mycoparasitic Interactions
Katarina Ihrmark, Nashwan Asmail, Wimal Ubhayasekera, Petter Melin, Jan Stenlid and Magnus Karlsson
Evolutionary Bioinformatics 2010:6 1-26
Original research | Published on 15 Mar 2010



A Comparative Taxonomy of Parallel Algorithms for RNA Secondary Structure Prediction
Ra’ed M. Al-Khatib, Rosni Abdullah and Nur’aini Abdul Rashid
Evolutionary Bioinformatics 2010:6 27-45
Original research | Published on 09 Apr 2010



Relative Codon Adaptation Index, a Sensitive Measure of Codon Usage Bias
Soohyun Lee, Seyeon Weon, Sooncheol Lee and Changwon Kang
Evolutionary Bioinformatics 2010:6 47-55
Original research | Published on 05 May 2010



An Application of Supertree Methods to Mammalian Mitogenomic Sequences
Véronique Campbell and François-Joseph Lapointe
Evolutionary Bioinformatics 2010:6 57-71
Original research | Published on 12 May 2010



Maximum Likelihood Analyses of 3,490 rbcL Sequences: Scalability of Comprehensive Inference Versus Group-Specific Taxon Sampling
Alexandros Stamatakis, Markus Göker and Guido W. Grimm
Evolutionary Bioinformatics 2010:6 73-90
Original research | Published on 24 May 2010



Molecular Phylogeny of Edge Hill Virus Supports its Position in the Yellow Fever Virus Group and Identifies a New Genetic Variant
Joanne Macdonald, Michael Poidinger, John S. Mackenzie, Richard C. Russell, Stephen Doggett, Annette K. Broom, Debra Phillips, Joseph Potamski, Geoff Gard, Peter Whelan, Richard Weir, Paul R. Young, Debra Gendle, Sheryl Maher, Ross T. Barnard and Roy A. Hall
Evolutionary Bioinformatics 2010:6 91-96
Original research | Published on 15 Jun 2010



A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA
Markus Göker, Guido W. Grimm, Alexander F. Auch, Ralf Aurahs and Michal Kučera
Evolutionary Bioinformatics 2010:6 97-112
Original research | Published on 09 Sep 2010



Identifying the Combinatorial Effects of Histone Modifications by Association Rule Mining in Yeast
Jiang Wang, Xianhua Dai, Qian Xiang, Yangyang Deng, Jihua Feng, Zhiming Dai and Caisheng He
Evolutionary Bioinformatics 2010:6 113-131
Original research | Published on 20 Sep 2010



Computational Identification of Anthocyanin-Specific Transcription Factors using a Rice Microarray and Maximum Boundary Range Algorithm
Chang Kug Kim, Shoshi Kikuchi, Jang Ho Hahn, Soo Chul Park, Yong Hwan Kim and Byun Woo Lee
Evolutionary Bioinformatics 2010:6 133-141
Original research | Published on 20 Oct 2010



EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics
Michael S. Barker, Katrina M. Dlugosch, Louie Dinh, R. Sashikiran Challa, Nolan C. Kane, Matthew G. King and Loren H. Rieseberg
Evolutionary Bioinformatics 2010:6 143-149
Original research | Published on 20 Oct 2010



DNA Barcodes of Arabian Partridge and Philby's Rock Partridge: Implications for Phylogeny and Species Identification
Haseeb Ahmad Khan, Ibrahim Abdulwahid Arif and Mohammad Shobrak
Evolutionary Bioinformatics 2010:6 151-158
Original research | Published on 05 Dec 2010



Where Does the Alignment Score Distribution Shape Come from?
Philippe Ortet and Olivier Bastien
Evolutionary Bioinformatics 2010:6 159-187
Original research | Published on 12 Dec 2010



PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences
Kessy Abarenkov, Leho Tedersoo, R. Henrik Nilsson, Kai Vellak, Irja Saar, Vilmar Veldre, Erast Parmasto, Marko Prous, Anne Aan, Margus Ots, Olavi Kurina, Ivika Ostonen, Janno Jõgeva, Siim Halapuu, Kadri Põldmaa, Märt Toots, Jaak Truu, Karl-Henrik Larsson and Urmas Kõljalg
Evolutionary Bioinformatics 2010:6 189-196
Original research | Published on 16 Dec 2010



Cost-Effective Cloud Computing: A Case Study Using the Comparative Genomics Tool, Roundup
Parul Kudtarkar, Todd F. DeLuca, Vincent A. Fusaro, Peter J. Tonellato and Dennis P. Wall
Evolutionary Bioinformatics 2010:6 197-203
Original research | Published on 22 Dec 2010



2009:5

REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era
Guy Leonard, Jamie R. Stevens and Thomas A. Richards
Evolutionary Bioinformatics 2009:5 1-4
Original research | Published on 06 May 2009



Evolution and Functional Diversification of the GLI Family of Transcription Factors in Vertebrates
Amir Ali Abbasi, Debbie K. Goode, Saneela Amir and Karl-Heinz Grzeschik
Evolutionary Bioinformatics 2009:5 5-13
Original research | Published on 18 May 2009



Phylogenetic Analyses Reveal Monophyletic Origin of the Ergot Alkaloid Gene dmaW in Fungi
Miao Liu, Daniel G. Panaccione and Christopher L. Schardl
Evolutionary Bioinformatics 2009:5 15-30
Original research | Published on 04 Jun 2009



Phylogenetic Applications of the Minimum Contradiction Approach on Continuous Characters
Marc Thuillard and Didier Fraix-Burnet
Evolutionary Bioinformatics 2009:5 33-46
Original research | Published on 11 Jun 2009



Initial Implementation of a Comparative Data Analysis Ontology
Francisco Prosdocimi, Brandon Chisham, Enrico Pontelli, Julie D. Thompson and Arlin Stoltzfus
Evolutionary Bioinformatics 2009:5 47-66
Original research | Published on 03 Jul 2009



A Mixture Model and a Hidden Markov Model to Simultaneously Detect Recombination Breakpoints and Reconstruct Phylogenies
Bastien Boussau, Laurent Guéguen and Manolo Gouy
Evolutionary Bioinformatics 2009:5 67-79
Original research | Published on 25 Jun 2009



A Comprehensive Analysis of Gene Expression Evolution Between Humans and Mice
Yupeng Wang and Romdhane Rekaya
Evolutionary Bioinformatics 2009:5 81-90
Original research | Published on 06 Jul 2009



PhyLIS: A Simple GNU/Linux Distribution for Phylogenetics and Phyloinformatics
Robert C. Thomson
Evolutionary Bioinformatics 2009:5 91-95
Original research | Published on 30 Jul 2009



On the Use of Bootstrapped Topologies in Coalescent-Based Bayesian MCMC Inference: A Comparison of Estimation and Computational Efficiencies
Allen G. Rodrigo, Peter Tsai and Helen Shearman
Evolutionary Bioinformatics 2009:5 97-105
Original research | Published on 31 Jul 2009



A Model for Protein Sequence Evolution Based on Selective Pressure for Protein Stability: Application to Hemoglobins
Lorraine Marsh
Evolutionary Bioinformatics 2009:5 107-118
Original research | Published on 27 Aug 2009



Genome-Wide Identification and Evolutionary Analysis of the Animal Specific ETS Transcription Factor Family
Zhipeng Wang and Qin Zhang
Evolutionary Bioinformatics 2009:5 119-131
Original research | Published on 02 Oct 2009



Snapshots of Tree Space
Zheng Wang, Francesc López-Giráldez and Jeffrey P. Townsend
Evolutionary Bioinformatics 2009:5 133-136
Original research | Published on 18 Jan 2010



Clustering Protein Sequences Using Affinity Propagation Based on an Improved Similarity Measure
Fan Yang, Qing-Xin Zhu, Dong-Ming Tang and Ming-Yuan Zhao
Evolutionary Bioinformatics 2009:5 137-146
Original research | Published on 22 Jan 2010



2008:4

Detecting Microsatellites in Genome Data: Variance in Definitions and Bioinformatic Approaches Cause Systematic Bias
Angelika Merkel and Neil J. Gemmell
Evolutionary Bioinformatics 2008:4 1-6
Original research | Published on 09 Feb 2008



Reverse Conservation Analysis Reveals the Specificity Determining Residues of Cytochrome P450 Family 2 (CYP 2)
Tai-Sung Lee
Evolutionary Bioinformatics 2008:4 7-16
Original research | Published on 09 Feb 2008



SPR Distance Computation for Unrooted Trees
Glenn Hickey, Frank Dehne, Andrew Rau-Chaplin and Christian Blouin
Evolutionary Bioinformatics 2008:4 17-27
Original research | Published on 09 Feb 2008



A Simple Derivation of the Distribution of Pairwise Local Protein Sequence Alignment Scores
Olivier Bastien
Evolutionary Bioinformatics 2008:4 41-45
Original research | Published on 14 Feb 2008



Why Should We Care About Molecular Coevolution?
Francisco M. Codoñer and Mario A. Fares
Evolutionary Bioinformatics 2008:4 29-38
Original research | Published on 14 Feb 2008



Comparative Evolutionary Histories of the Fungal Chitinase Gene Family Reveal Non-Random Size Expansions and Contractions due to Adaptive Natural Selection
Magnus Karlsson and Jan Stenlid
Evolutionary Bioinformatics 2008:4 47-60
Original research | Published on 18 Mar 2008



Expected Anomalies in the Fossil Record
Mareike Fischer and Mike Steel
Evolutionary Bioinformatics 2008:4 61-67
Original research | Published on 18 Mar 2008



How to Summarize Estimates of Ancestral Divergence Times
David A. Morrison
Evolutionary Bioinformatics 2008:4 75-95
Original research | Published on 18 Mar 2008



The ABCs of MGR with DCJ
Zaky Adam and David Sankoff
Evolutionary Bioinformatics 2008:4 69-74
Original research | Published on 10 Apr 2008



Assessing the Evolution of Gene Expression Using Microarray Data
Owen Z. Woody, Andrew C. Doxey and Brendan J. McConkey
Evolutionary Bioinformatics 2008:4 139-152
Original research | Published on 24 Apr 2008



Identifying Coevolving Partners from Paralogous Gene Families
Chen-Hsiang Yeang
Evolutionary Bioinformatics 2008:4 97-107
Original research | Published on 24 Apr 2008



Dissection of Functional Residues in Receptor Activity-Modifying Proteins Through Phylogenetic and Statistical Analyses
Alfonso Benítez-Páez and Sonia Cárdenas-Brito
Evolutionary Bioinformatics 2008:4 153-169
Original research | Published on 28 Apr 2008



Strategies for Reliable Exploitation of Evolutionary Concepts in High Throughput Biology
Anthony Levasseur, Pierre Pontarotti, Olivier Poch and Julie D. Thompson
Evolutionary Bioinformatics 2008:4 121-137
Original research | Published on 08 May 2008



Examining Ancient Inter-domain Horizontal Gene Transfer
Francisca C. Almeida, Magdalena Leszczyniecka, Paul B. Fisher and Rob DeSalle
Evolutionary Bioinformatics 2008:4 109-119
Original research | Published on 09 May 2008



Exploring the Evolutionary History of the Differentially Expressed Genes between Human Populations: Action of Recent Positive Selection
Wei Zhang and M. Eileen Dolan
Evolutionary Bioinformatics 2008:4 171-179
Original research | Published on 15 May 2008



Maximum Gene-Support Tree
Yunfeng Shan and Xiu-Qing Li
Evolutionary Bioinformatics 2008:4 181-191
Original research | Published on 15 May 2008



Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification
R. Henrik Nilsson, Erik Kristiansson, Martin Ryberg, Nils Hallenberg and Karl ­Henrik Larsson
Evolutionary Bioinformatics 2008:4 193-201
Original research | Published on 26 May 2008



Electrostatic and Functional Analysis of the Seven-Bladed WD β-Propellers
Najl V Valeyev, A Kristina Downing, John Sondek and Charlotte Deane
Evolutionary Bioinformatics 2008:4 203-216
Original research | Published on 13 Jun 2008



Testing the Accuracy of Eukaryotic Phylogenetic Profiles for Prediction of Biological Function
Saurav Singh and Dennis P. Wall
Evolutionary Bioinformatics 2008:4 217-223
Original research | Published on 18 Jun 2008



Estimation of Genetic Effects and Genotype-Phenotype Maps
Arnaud Le Rouzic and José M. Álvarez-Castro
Evolutionary Bioinformatics 2008:4 225-235
Original research | Published on 28 Jun 2008



Minimum Contradiction Matrices in Whole Genome Phylogenies
Marc Thuillard
Evolutionary Bioinformatics 2008:4 237-247

Original research | Published on 21 Jul 2008



Evidence for a Complex Mosaic Genome Pattern in a Full-length Hepatitis C Virus Sequence
R.S. Ross, J. Verbeeck, S. Viazov, P. Lemey, M. Van Ranst and M. Roggendorf
Evolutionary Bioinformatics 2008:4 249-254
Original research | Published on 30 Oct 2008



Inconsistent Distances in Substitution Matrices can be Avoided by Properly Handling Hydrophobic Residues
J. Baussand and A. Carbone
Evolutionary Bioinformatics 2008:4 255-261
Original research | Published on 09 Oct 2008



Bayesian, Maximum Parsimony and UPGMA Models for Inferring the Phylogenies of Antelopes Using Mitochondrial Markers
Haseeb A. Khan, Ibrahim A. Arif, Ali H. Bahkali, Ahmad H. Al Farhan and Ali A. Al Homeidan
Evolutionary Bioinformatics 2008:4 263-270
Original research | Published on 06 Oct 2008



The Austronesian Basic Vocabulary Database: From Bioinformatics to Lexomics
Simon J. Greenhill, Robert Blust and Russell D. Gray
Evolutionary Bioinformatics 2008:4 271-283
Original research | Published on 03 Nov 2008



2007:3

The 2006 NESCent Phyloinformatics Hackathon: A Field Report
Hilmar Lapp, Sendu Bala, James P. Balhoff, Amy Bouck, Naohisa Goto, Mark Holder, Richard Holland, Alisha Holloway, Toshiaki Katayama, Paul O. Lewis, Aaron J. Mackey, Brian I. Osborne, William H. Piel, Sergei L. Kosakovsky Pond, Art F.Y. Poon, Wei-Gang Qiu et al
Evolutionary Bioinformatics 2007:3 287-296
Original research | Published on 14 Dec 2007



Identification of Conflicting Selective Effects on Highly Expressed Genes
Paul G. Higgs, Weilong Hao and G. Brian Golding
Evolutionary Bioinformatics 2007:3 1-13
Original research | Published on 14 Feb 2007



MapToGenome: A Comparative Genomic Tool that Aligns Transcript Maps to Sequenced Genomes
Srikrishna Putta, Jeramiah J. Smith, Chuck Staben and S. Randal Voss
Evolutionary Bioinformatics 2007:3 15-25
Original research | Published on 14 Feb 2007



On the Adaptive Design Rules of Biochemical Networks in Evolution
Bor-Sen Chen, Wan-Shian Wu, Wei-Sheng Wu and Wen-Hsiung Li
Evolutionary Bioinformatics 2007:3 27-39
Original research | Published on 28 Feb 2007



Mlcoalsim: Multilocus Coalescent Simulations
Sebastian E. Ramos-Onsins and Thomas Mitchell-Olds
Evolutionary Bioinformatics 2007:3 41-44
Original research | Published on 02 Mar 2007



Mammoth and Elephant Phylogenetic Relationships: Mammut Americanum, the Missing Outgroup
Ludovic Orlando, Catherine Hänni and Christophe J. Douady
Evolutionary Bioinformatics 2007:3 45-51
Original research | Published on 29 Mar 2007



An Improved Implementation of Codon Adaptation Index
Xuhua Xia
Evolutionary Bioinformatics 2007:3 53-58
Original research | Published on 17 May 2007



A Reduction Algorithm for Computing The Hybridization Number of Two Trees
Magnus Bordewich, Simone Linz, Katherine St. John and Charles Semple
Evolutionary Bioinformatics 2007:3 86-98
Original research | Published on 30 May 2007



Fast Genes and Slow Clades: Comparative Rates of Molecular Evolution in Mammals
Olaf R. P. Bininda-Emonds
Evolutionary Bioinformatics 2007:3 59-85
Original research | Published on 31 May 2007



Choosing and Using Introns in Molecular Phylogenetics
Simon Creer
Evolutionary Bioinformatics 2007:3 99-108
Original research | Published on 14 Jun 2007



Environmental Quality, Developmental Plasticity and the Thrifty Phenotype: A Review of Evolutionary Models
Jonathan CK Wells
Evolutionary Bioinformatics 2007:3 109-120
Original research | Published on 19 Jun 2007



Prediction of Protein-protein Interactions on the Basis of Evolutionary Conservation of Protein Functions
Ekaterina Kotelnikova, Andrey Kalinin, Anton Yuryev, and Sergei Maslov
Evolutionary Bioinformatics 2007:3 197-206
Original research | Published on 08 Aug 2007



Characterization and Evolution of the Cell Cycle-Associated Mob Domain-Containing Proteins in Eukaryotes
Nicola Vitulo, Alessandro Vezzi, Giulio Galla, Sandra Citterio, Giada Marino, Benedetto Ruperti, Monica Zermiani, Emidio Albertini, Giorgio Valle and Gianni Barcaccia
Evolutionary Bioinformatics 2007:3 121-158
Original research | Published on 08 Aug 2007



The GC Skew Index: A Measure of Genomic Compositional Asymmetry and the Degree of Replicational Selection
Kazuharu Arakawa and Masaru Tomita
Evolutionary Bioinformatics 2007:3 159-168
Original research | Published on 06 Sep 2007



Interactions Between SNP Alleles at Multiple Loci and Variation in Skin Pigmentation in 122 Caucasians
Sumiko Anno, Takashi Abe, Koichi Sairyo, Susumu Kudo, Takushi Yamamoto, Koretsugu Ogata and Vijay K. Goel
Evolutionary Bioinformatics 2007:3 169-178
Original research | Published on 06 Sep 2007



Identifcation of Novel Retroid Agents in Danio rerio, Oryzias latipes, Gasterosteus aculeatus and Tetraodon nigroviridis
Holly A. Basta, Alex J. Buzak and Marcella A. McClure
Evolutionary Bioinformatics 2007:3 179-195
Original research | Published on 06 Sep 2007



Gathering Computational Genomics and Proteomics to Unravel Adaptive Evolution
Agostinho Antunes and Maria João Ramos
Evolutionary Bioinformatics 2007:3 207-209
Original research | Published on 06 Sep 2007



Genome Signatures, Self-Organizing Maps and Higher Order Phylogenies: A Parametric Analysis
Derek Gatherer
Evolutionary Bioinformatics 2007:3 211-236
Original research | Published on 17 Sep 2007



Hedging Our Bets: The Expected Contribution of Species to Future Phylogenetic Diversity
Mike Steel, Aki Mimoto and Arne Ø. Mooers
Evolutionary Bioinformatics 2007:3 237-244
Original research | Published on 25 Sep 2007



Phylogenomic Analysis Reveals Extensive Phylogenetic Mosaicism in the Human GPCR Superfamily
Robin G. Allaby and Mathew Woodwark
Evolutionary Bioinformatics 2007:3 357-370
Original research | Published on 26 Sep 2007



Non-Molecular-Clock-Like Evolution following Viral Origins in Homo sapiens
Wendy Mok, Kelly Seto and Jon Stone
Evolutionary Bioinformatics 2007:3 263-266
Original research | Published on 26 Sep 2007



Underlying Principles of Natural Selection in Network Evolution: Systems Biology Approach
Bor-Sen Chen and Wei-Sheng Wu
Evolutionary Bioinformatics 2007:3 245-262
Original research | Published on 26 Sep 2007



Selection Effects on the Positioning of Genes and Gene Structures from the Interplay of Replication and Transcription in Bacterial Genomes
Kazuharu Arakawa and Masaru Tomita
Evolutionary Bioinformatics 2007:3 279-286
Original research | Published on 09 Oct 2007



Minimizing Contradictions on Circular Order of Phylogenic Trees
Marc Thuillard
Evolutionary Bioinformatics 2007:3 267-277
Original research | Published on 11 Oct 2007



An Insulin-Like Modular Basis for the Evolution of Glucose Transporters (GLUT) with Implications for Diabetes
Robert Root-Bernstein
Evolutionary Bioinformatics 2007:3 317-331
Original research | Published on 15 Oct 2007



Structural Evolution of the ABC Transporter Subfamily B
Flanagan, J.U. and Huber, T.
Evolutionary Bioinformatics 2007:3 309-316
Original research | Published on 08 Nov 2007



Efficient Tree Searches with Available Algorithms
Gonzalo Giribet
Evolutionary Bioinformatics 2007:3 341-356
Original research | Published on 12 Nov 2007



Phylogenetic Study of the Evolution of PEP-Carboxykinase
Sanjukta Aich and Louis T.J. Delbaere
Evolutionary Bioinformatics 2007:3 333-340
Original research | Published on 11 Dec 2007



Evolution of the Influenza A Virus: Some New Advances
Raul Rabadan and Harlan Robins
Evolutionary Bioinformatics Online 2007:3 299-307
Original research | Published on 30 Jan 2008



2006:2

Improved Heuristics for Minimum-Flip Supertree Construction
Duhong Chen, Oliver Eulenstein, David Fernández-Baca and J.Gordon Burleigh
Evolutionary Bioinformatics 2006:2 347-356
Original research | Published on 28 Feb 2007



Outsourcing the Nucleus: Nuclear Pore Complex Genes are no Longer Encoded in Nucleomorph Genomes
Nadja Neumann, Daniel C. Jeffares and Anthony M. Poole
Evolutionary Bioinformatics 2006:2 23-34
Original research | Published on 27 Feb 2007 | Highly accessed (previous month)



Topological Bias in Distance-Based Phylogenetic Methods: Problems with Over- and Underestimated Genetic Distances
Xuhua Xia
Evolutionary Bioinformatics 2006:2 333-345
Original research | Published on 26 Feb 2007



Pattern-Based Phylogenetic Distance Estimation and Tree Reconstruction
Michael Höhl, Isidore Rigoutsos and Mark A. Ragan
Evolutionary Bioinformatics 2006:2 359-375
Original research | Published on 25 Feb 2007



Multiple Property Tolerance Analysis for the Evaluation of Missense Mutations
Tai-Sung Lee, Steven J. Potts, Matthew J. McGinniss and Charles M. Strom
Evolutionary Bioinformatics 2006:2 321-332
Original research | Published on 24 Feb 2007



A Fast and Specific Alignment Method for Minisatellite Maps
Sèverine Bérard, François Nicolas, Jérôme Buard, Olivier Gascuel and Eric Rivals
Evolutionary Bioinformatics 2006:2 303-320
Original research | Published on 22 Feb 2007



Genome Halving with an Outgroup
Chunfang Zheng, Qian Zhu and David Sankoff
Evolutionary Bioinformatics 2006:2 295-302
Original research | Published on 21 Feb 2007



Estimating the Relative Order of Speciation or Coalescence Events on a Given Phylogeny
Tanja Gernhard, Daniel Ford, Rutger Vos and Mike Steel
Evolutionary Bioinformatics 2006:2 285-293
Original research | Published on 20 Feb 2007



The Role of the Phylogenetic Diversity Measure, PD, in Bio-informatics: Getting the Definition Right
Daniel P. Faith
Evolutionary Bioinformatics 2006:2 277-283
Original research | Published on 19 Feb 2007



Co-evolutionary Rates of Functionally Related Yeast Genes
Leonardo Mariño-Ramírez, Olivier Bodenreider, Natalie Kantz and I. King Jordan
Evolutionary Bioinformatics 2006:2 271-276
Original research | Published on 18 Feb 2007



A Nuclear Ribosomal DNA Phylogeny of Acer Inferred with Maximum Likelihood, Splits Graphs, and Motif Analysis of 606 Sequences
Guido W. Grimm, Susanne S. Renner, Alexandros Stamatakis and Vera Hemleben
Evolutionary Bioinformatics 2006:2 7-22
Original research | Published on 17 Feb 2007



Minimum Conflict Individual Haplotyping from SNP Fragments and Related Genotype
Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu and Wei Zhang
Evolutionary Bioinformatics 2006:2 261-270
Original research | Published on 16 Feb 2007



Gaussian Quadrature Formulae for Arbitrary Positive Measures
Andrew D. Fernandes and William R. Atchley
Evolutionary Bioinformatics 2006:2 251-259
Original research | Published on 15 Feb 2007



LASER: A Maximum Likelihood Toolkit for Detecting Temporal Shifts in Diversification Rates From Molecular Phylogenies
Daniel L. Rabosky
Evolutionary Bioinformatics 2006:2 247-250
Original research | Published on 14 Feb 2007



Total Evidence, Average Consensus and Matrix Representation with Parsimony: What a Difference Distances Make
Claudine Levasseur and François-Joseph Lapointe
Evolutionary Bioinformatics 2006:2 1-5
Original research | Published on 13 Feb 2007



Estimating Population Parameters using the Structured Serial Coalescent with Bayesian MCMC Inference when some Demes are Hidden
Greg Ewing and Allen Rodrigo
Evolutionary Bioinformatics 2006:2 227-235
Original research | Published on 12 Feb 2007



Unravelling Selection Shifts Among Foot-and-Mouth Disease Virus (FMDV) Serotypes
Damien C. Tully and Mario A. Fares
Evolutionary Bioinformatics 2006:2 211-225

Original research | Published on 11 Feb 2007



PIRSF Family Classification System for Protein Functional and Evolutionary Analysis
Anastasia N. Nikolskaya, Cecilia N. Arighi, Hongzhan Huang, Winona C. Barker and Cathy H. Wu
Evolutionary Bioinformatics 2006:2 197-209
Original research | Published on 10 Feb 2007



Spectral Analysis of Sequence Variability in Basic-Helix-loop-helix (bHLH) Protein Domains
Zhi Wang and William R. Atchley
Evolutionary Bioinformatics 2006:2 187-196
Original research | Published on 09 Feb 2007



CoMET: A Mesquite package for comparing models of continuous character evolution on phylogenies
Chunghau Lee, Sigal Blay, Arne Ø. Mooers, Ambuj Singh, Todd H. Oakley
Evolutionary Bioinformatics 2006:2 183-186
Original research | Published on 07 Feb 2007



MBEToolbox 2.0: An enhanced version of a MATLAB toolbox for Molecular Biology and Evolution
James J. Cai, David K. Smith, Xuhua Xia and Kwok-yung Yuen
Evolutionary Bioinformatics 2006:2 179-182
Original research | Published on 06 Feb 2007



Modelling prokaryote gene content
Matthew Spencer, Edward Susko, and Andrew J. Roger
Evolutionary Bioinformatics 2006:2 157-178
Original research | Published on 05 Feb 2007



Assessing the Applicability of the GTR Nucleotide Substitution Model Through Simulations
Laurent Gatto, Daniele Catanzaro and Michel C. Milinkovitch
Evolutionary Bioinformatics 2006:2 145-155
Original research | Published on 04 Feb 2007



Using minimum bootstrap support for splits to construct confidence regions for trees
Edward Susko
Evolutionary Bioinformatics 2006:2 129-143
Original research | Published on 03 Feb 2007



3 UTR-located ALU Elements: Donors of Potetial miRNA Target Sites and Mediators of Network miRNA-based Regulatory Interactions
Evelina Daskalova, Vesselin Baev, Ventsislav Rusinov, and Ivan Minkov
Evolutionary Bioinformatics 2006:2 103-120
Original research | Published on 18 Jan 2007



Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges
Daniel P. Faith, Andrew M. Baker
Evolutionary Bioinformatics 2006:2 121-128
Original research | Published on 17 Feb 2007



Functionality and the evolution of marginal stability in proteins: Inferences from lattice simulations
Paul D. Williams, David D. Pollock and Richard A. Goldstein
Evolutionary Bioinformatics 2006:2 91-101
Original research | Published on 16 Jan 2007



Evolution, Bioinformatics and Evolutionary Bioinformatics Online
Dr Mark Pagel
Evolutionary Bioinformatics 2006:2 357-358
Original research | Published on 15 Jan 2007



Positional Homology in Bacterial Genomes
Ingrid J. Burgetz, Salimah Shariff, Andy Pang and Elisabeth R. M. Tillier
Evolutionary Bioinformatics 2006:2 77-90
Original research | Published on 14 Jan 2007



Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes
Howard A. Ross, David C. Nickle, Yi Liu, Laura Heath, Mark A. Jensen, Allen G. Rodrigo and James I. Mullins
Evolutionary Bioinformatics 2006:2 53-76
Original research | Published on 13 Jan 2007



Finding common protein interaction patterns across organisms
Mirco Gerke, Erich Bornberg-Bauer, Xiaoyi Jiang and Georg Fuellen
Evolutionary Bioinformatics 2006:2 45-52
Original research | Published on 12 Jan 2007



Coevolution of exploiter specialization and victim mimicry can be cyclic and saltational
Niclas Norrström, Wayne M. Getz, Noél M.A. Holmgren
Evolutionary Bioinformatics 2006:2 35-43
Original research | Published on 11 Jan 2007



A new effective method for estimating missing values in the sequence data prior to phylogenetic analysis
Abdoulaye Baniré Diallo, François-Joseph Lapointe and Vladimir Makarenkov
Evolutionary Bioinformatics 2006:2 237-246
Original research | Published on 01 Feb 2007



The Rv3799–Rv3807 Gene Cluster in Mycobacterium Tuberculosis Genome Corresponds to the ‘Ancient Conserved Region’ in CMN Mycolyltransferases
Hemalatha G. Ramulu, Adindla Swathi and Lalitha Guruprasad
Evolutionary Bioinformatics Online 2006:2 377-385
Original research | Published on 27 Feb 2007



2005:1

Why Bacteriophage Encode Exotoxins and other Virulence Factors
Stephen T. Abedon and Jeffrey T. LeJeune
Evolutionary Bioinformatics Online 2005:1 97-110
Original research | Published on 28 Feb 2007



The identification of functional motifs in temporal gene expression analysis
Jiuzhou Song, Jaime Bjarnason and Michael G. Surette
Evolutionary Bioinformatics Online 2005:1 84-96
Original research | Published on 27 Feb 2007



MySSP: Non-stationary evolutionary sequence simulation, including indels
Michael S. Rosenberg
Evolutionary Bioinformatics Online 2005:1 81-83
Original research | Published on 26 Feb 2007



Estimation of Phylogeny Using a General Markov Model
Vivek Jayaswal, Lars S. Jermiin and John Robinson
Evolutionary Bioinformatics Online 2005:1 62-80
Original research | Published on 25 Feb 2007



Evolution of proteins and proteomes: a phylogenetics approach
Toni Gabaldón
Evolutionary Bioinformatics Online 2005:1 51-61
Original research | Published on 24 Feb 2007



Arlequin (version 3.0): An integrated software package for population genetics data analysis
Laurent Excoffier, Guillaume Laval and Stefan Schneider
Evolutionary Bioinformatics Online 2005:1 47-50
Original research | Published on 23 Feb 2007



ALFRED: An Allele Frequency Database for Microevolutionary Studies
Haseena Rajeevan, Kei-Hoi Cheung, Rohit Gadagkar, Shannon Stein, Usha Soundararajan, Judith R Kidd, Andrew J Pakstis, Perry L Miller, and Kenneth K Kidd
Evolutionary Bioinformatics Online 2005:1 1-10
Original research | Published on 22 Feb 2007



Phylogenetic biodiversity assessment based on systematic nomenclature
Ross H Crozier, Lisa J Dunnett and Paul-Michael Agapow
Evolutionary Bioinformatics Online 2005:1 11-36
Original research | Published on 21 Feb 2007



Fast Structural Search in Phylogenetic Databases
Jason T. L. Wang, Huiyuan Shan, Dennis Shasha and William H. Piel
Evolutionary Bioinformatics Online 2005:1 37-46
Original research | Published on 20 Feb 2007





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