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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: 1.404 (2015)

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.

Databases & Indexes:



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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



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



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



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



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
Methodology | Published on 30 Aug 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



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



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



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



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



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



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



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
Software or database review | Published on 10 Mar 2011



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



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



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



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



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
Short Report | Published on 20 Oct 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



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



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
Short Report | Published on 15 Jun 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



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



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



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



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



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
Methodology | Published on 22 Jan 2010



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



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



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



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



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



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



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
Methodology | 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
Methodology | Published on 25 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



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



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



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



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



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
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
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
Published on 06 Oct 2008



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

Published on 21 Jul 2008



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



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





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