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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Polymorphism of 11 Y Chromosome Short Tandem Repeat Markers among Malaysian Aborigines
Sofia Sakina Mohd Yussup, Marlia Marzukhi, Badrul Munir Md-Zain, Kamaruddin Mamat, Farida Zuraina Mohd Yusof
Evolutionary Bioinformatics 2017:13 1176934317735318
Original Research | Published on 17 Oct 2017

MGUPGMA: A Fast UPGMA Algorithm With Multiple Graphics Processing Units Using NCCL
Guan-Jie Hua, Che-Lun Hung, Chun-Yuan Lin, Fu-Che Wu, Yu-Wei Chan, Chuan Yi Tang
Evolutionary Bioinformatics 2017:13 1176934317734220
Review | Published on 04 Oct 2017

A Modified Mean Gray Wolf Optimization Approach for Benchmark and Biomedical Problems
Narinder Singh, SB Singh
Evolutionary Bioinformatics 2017:13 1176934317729413
Original Research | Published on 11 Sep 2017

Hierarchical Association Coefficient Algorithm: New Method for Genome-Wide Association Study
Bongsong Kim
Evolutionary Bioinformatics 2017:13 1176934317713004
Original Research | Published on 31 Aug 2017

Optimized Next-Generation Sequencing Genotype-Haplotype Calling for Genome Variability Analysis
Javier Navarro, Bruno Nevado, Porfidio Hernández, Gonzalo Vera, Sebastián E Ramos-Onsins
Evolutionary Bioinformatics 2017:13 1176934317723884
Original Research | Published on 24 Aug 2017

Complete Mitochondrial Genomes of the Cherskii’s Sculpin and Siberian Taimen Reveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome
Evgeniy S Balakirev, Pavel A Saveliev, Francisco J Ayala
Evolutionary Bioinformatics 2017:13 1176934317726783
Short Report | Published on 24 Aug 2017

Popmarker: Identifying Phylogenetic Markers at the Population Level
Huei-Mien Ke, Chun-Ping Yu, Yu-Ching Liu, Isheng J Tsai
Evolutionary Bioinformatics 2017:13 1176934317724404
Review | Published on 16 Aug 2017

Embedded-Based Graphics Processing Unit Cluster Platform for Multiple Sequence Alignments
Jyh-Da Wei, Hui-Jun Cheng, Chun-Yuan Lin, Jin Ye, Kuan-Yu Yeh
Evolutionary Bioinformatics 2017:13 1176934317724764
Review | Published on 08 Aug 2017

Identification of very small open reading frames in the genomes of Holmes Jungle virus, Ord River virus, and Wongabel virus of the genus , family
Aneta Gubala, Susan Walsh, Jane McAllister, Richard Weir, Steven Davis, Lorna Melville, Ian Mitchell, Dieter Bulach, Penny Gauci, Alex Skvortsov, David Boyle
Evolutionary Bioinformatics 2017:13 1176934317713484
Review | Published on 11 Jul 2017

RapaNet: A Web Tool for the Co-Expression Analysis of Brassica rapa 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

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

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

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

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

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

Numericware i: Identical by State Matrix Calculator
Bongsong Kim, William D Beavis
Evolutionary Bioinformatics 2017:13 1176934316688663
Software or database review | 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

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

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

Evolutionary Bioinformatics 2017:13 1176934316688670
Editorial | Published on 30 Jan 2017

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
Review | Published on 10 Jan 2017

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

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
Short Report | Published on 12 Dec 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

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

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

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 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

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

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

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

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
Software or database review | Published on 02 Oct 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

Virus Discovery Using Tick Cell Lines
Lesley Bell-Sakyi and Houssam Attoui
Evolutionary Bioinformatics 2016:Suppl. 2 31-34
Short Commentary | Published on 15 Sep 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
Commentary | Published on 14 Sep 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

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

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

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

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

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

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
Review | Published on 20 Jun 2016
This article is part of the special collection Bioinformatics Methods and Applications for Big Metagenomics Data

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

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

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

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

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
Technical Advance | Published on 31 May 2016
This article is part of the special collection Bioinformatics Methods and Applications for Big Metagenomics Data

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
Correction | Published on 29 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

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
Review | Published on 12 May 2016
This article is part of the special collection Bioinformatics Methods and Applications for Big Metagenomics Data

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

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

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

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

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

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
Short Report | Published on 03 Apr 2016
This article is part of the special collection Bioinformatics Methods and Applications for Big Metagenomics Data

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
Technical Advance | Published on 25 Feb 2016

Using UNIFORMAT and GENE[RATE] to Analyze Data with Ambiguities in Population Genetics
José Manuel Nunes
Evolutionary Bioinformatics 2015:Suppl. 2 19-26
Methodology | Published on 21 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
Technical Advance | Published on 10 Feb 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

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

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

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

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

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

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
Editorial | Published on 14 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

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
Software or Database Review | Published on 11 Jan 2016

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

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

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

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

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

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

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

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

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
Review | Published on 04 Oct 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
Review | Published on 13 Sep 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
Published on 01 Sep 2015

How Many Genes are Needed to Resolve Phylogenetic Incongruence?
Bin Ai and Ming Kang
Evolutionary Bioinformatics 2015:11 185-188
Rapid Communication | Published on 10 Aug 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
Review | Published on 05 Aug 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

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

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

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

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

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

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
Technical Advance | Published on 14 Jun 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

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
Technical Advance | Published on 24 May 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

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
Methodology | Published on 27 Apr 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

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
Software or database review | Published on 16 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
Software or database review | Published on 12 Mar 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

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

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
Methodology | Published on 23 Feb 2015

windex: Analyzing Convergent Evolution Using the Wheatsheaf Index in R
Kevin Arbuckle and Amanda Minter
Evolutionary Bioinformatics 2015:11 11-14
Short Report | Published on 12 Feb 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
Methodology | Published on 26 Jan 2015

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
Corrigendum | Published on 14 Jan 2015

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

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

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

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

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

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

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

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

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

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
Rapid Communication | Published on 03 Aug 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

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

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

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

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

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

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

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

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

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
Short Report | Published on 06 Feb 2014

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

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

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

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
Methodology | Published on 13 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

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

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
Methodology | Published on 29 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

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

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

POPBAM: Tools for Evolutionary Analysis of Short Read Sequence Alignments
Daniel Garrigan
Evolutionary Bioinformatics 2013:9 343-353
Technical Advance | 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
Software or database review | Published on 01 Sep 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

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

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

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
Methodology | Published on 28 Jul 2013

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