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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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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
Published on 26 May 2008



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



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



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



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



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



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



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
Software or database review | Published on 14 Mar 2012 | Video abstract



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



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



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
Short Report | Published on 20 Oct 2010



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



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
Published on 14 Dec 2007



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



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
Software or database review | Published on 16 Dec 2010



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



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



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



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
Published on 15 May 2008



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
Short Report | Published on 22 Dec 2010



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



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



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



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



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



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
Published on 06 Sep 2007



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



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



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



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



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



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



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



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



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



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
Published on 06 Oct 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
Published on 09 May 2008



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



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



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



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



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



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
Short Report | Published on 06 May 2009



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



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 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



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



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



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



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
Published on 24 Apr 2008





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