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2009

Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L (2009) Fast Statistical Alignment. PLoS Comput Biol 5:e1000392. ( link)
Dwivedi B and Gadagkar SR (2009) Phylogenetic Inference under Varying Proportions of Indel-Induced Alignment Gaps. BMC Evolutionary Biology 9:211 ( link)
Dwivedi B and Gadagkar SR (2009) The impact of sequence parameter values on phylogenetic accuracy. Biology and Medicine 1:50-62 ( link)
Fletcher W, Yang Z (2009) INDELible: A Flexible Simulator of Biological Sequence Evolution. Molecular Biolology and Evolution 26(8):1879-1888 ( link)
He X, Ling X, Sinha S, (2009) Alignment and Prediction of cis-Regulatory Modules Based on a Probabilistic Model of Evolution. PLoS Comput Biol 5: e1000299. ( link)
Som A (2009) ML or NJ-MCL? A comparison between two robust phylgenetic methods. Computational Biology and Chemistry 33:373-378 ( link)
Wang L, Leebens-Mack J, Wall P, Beckmann K, dePamphilis C, Warnow T (2009) The Impact of Multiple Protein Sequence Alignment on Phylogenetic Estimation. IEEE Transactions on Computational Biology and Bioinformatics Advanced Access ( link)

Dress AW, Flamm C, Fritzsch G, Grünewald S, Kruspe M, Prohaska SJ, Stadler PF (2008) Noisy: Identification of problematic columns in multiple sequence alignments. Algorithms Mol Biol. 3:7 ( link)
Hall B (2008) Simulating DNA Coding Sequence Evolution with EvolveAGene 3. Molecular Biology and Evolution 25(4):688-695 ( link)
Spagna JC and Alvarez-Padilla F (2008) Finding an upper limit for gap costs in direct optimization parsimony. Cladistics 5:787-801 ( link)
Sundberg K, O'Connor T, Carroll H, Clement M, and Snell Q (2008) Parsimony accelerated Maximum Likelihood searches. International Journal of Computational Biology and Drug Design 1(1):74-87 ( link)
Varadarajan A, Bradley RK, and Holmes IH (2008) Tools for simulating evolution of aligned genomic regions with integrated parameter estimation. Genome Biology 9:R147 ( link)
Yang K and Zhang L (2008) Performance comparison between k-tuple distance and four model-based distances in phylogenetic tree reconstruction. Nucleic Acids Research 36(5):e33-e33 ( link)
Zaki SAH, Jordan WC, Reichard M, Przybylski M, and Smith C (2008) A morphological and genetic analysis of the European bitterling species complex. Biological Journal of the Linnean Society 95(2):337-347 ( link)

Cartwright RA (2007) Ngila: global pairwise alignments with logarithmic and affine gap costs. Bioinformatics 23(11):1427-1428 ( link)
Hall B (2007) EvolveAGene 3: A DNA coding sequence evolution simulation program. Nature Precedings ( link)
Huang W, Nevins JR, and Ohler U (2007) Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools. Genome Biology 8:R225 ( link)
Kim J and Sinha S (2007) Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment. Bioinformatics 23(3):289-297 ( link)
Pavesi G, Zambelli F, and Pesole G (2007) WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences. BMC Bioinformatics 8:46 ( link)
Sinha S and He X (2007) MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis-Regulatory Modules. PLoS Comput Biol 3(11): e216 ( link)
Shaw J et al. (2007) Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. American Journal of Botany 94: 275-288 ( link)
Sundberg K, O'Connor T, Carroll H, Clement M, and Snell Q (2007) Using Parsimony to Guide Maximum Likelihood Searches. Bioinformatics and Bioengineering, Proceedings of the 7th IEEE International Conference on, 774-779 ( link)

Cartwright RA (2006) Logarithmic gap costs decrease alignment accuracy. BMC Bioinformatics 7:527 ( link)
Morrison DA (2006) L. A. S. JOHNSON REVIEW No. 8. Multiple sequence alignment for phylogenetic purposes. Australian Systematic Botany 19(6): 479–539 ( link)
Nuin PAS et al. (2006) The accuracy of several multiple sequence alignment programs for proteins. BMC Bioinformatics 7:471 ( link)
Strope CL et al. (2006) Indel-Seq-Gen: A New Protein Family Simulator Incorporating Domains, Motifs, and Indels. Molecular Biology and Evolution Advance Access published on December 8 ( link)

Cartwright RA (2005) DNA Assembly With Gaps (Dawg): Simulating Sequence Evolution. Bioinformatics 21 (Suppl. 3): iii31-iii38 ( link).
Elhaik E, Sabath N, and Graur D (2005) The "Inverse Relationship Between Evolutionary Rate and age of Mammalian Genes" is an Artifact of Increased Genetic Distance with Rate of Evolution and Time of Divergence. Molecular Biology and Evolution (Advance Access 9/8) ( link).
Rosenberg MS (2005) MySSP: Non-stationary evolutionary sequence simulation, including indels. Evolutionary Bioinformatics Online 1: 51-53 ( link).
Theobald DL and Wuttke DS (2005) Divergent evolution within protein superfolds inferred from profile-based phylogenetics. Journal of Molecular Biology 354(3): 722-737 ( link).