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PyEvolve: a toolkit for statistical modelling of molecular evolution.

Butterfield A, Vedagiri V, Lang E, Lawrence C, Wakefield MJ, Isaev A, Huttley GA.

BMC Bioinformatics. 2004 Jan 5;5:1.


BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology.

Villaverde AF, Henriques D, Smallbone K, Bongard S, Schmid J, Cicin-Sain D, Crombach A, Saez-Rodriguez J, Mauch K, Balsa-Canto E, Mendes P, Jaeger J, Banga JR.

BMC Syst Biol. 2015 Feb 20;9:8. doi: 10.1186/s12918-015-0144-4.


FASTAptamer: A Bioinformatic Toolkit for High-throughput Sequence Analysis of Combinatorial Selections.

Alam KK, Chang JL, Burke DH.

Mol Ther Nucleic Acids. 2015 Mar 3;4:e230. doi: 10.1038/mtna.2015.4.


GeLL: a generalized likelihood library for phylogenetic models.

Money D, Whelan S.

Bioinformatics. 2015 Feb 27. pii: btv126. [Epub ahead of print]


CodABC: a computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate Bayesian computation.

Arenas M, Lopes JS, Beaumont MA, Posada D.

Mol Biol Evol. 2015 Apr;32(4):1109-12. doi: 10.1093/molbev/msu411. Epub 2015 Jan 9.


Development and application of new quality model for software projects.

Karnavel K, Dillibabu R.

ScientificWorldJournal. 2014;2014:491246. doi: 10.1155/2014/491246. Epub 2014 Nov 16.


The phylogenetic likelihood library.

Flouri T, Izquierdo-Carrasco F, Darriba D, Aberer AJ, Nguyen LT, Minh BQ, Von Haeseler A, Stamatakis A.

Syst Biol. 2015 Mar;64(2):356-62. doi: 10.1093/sysbio/syu084. Epub 2014 Oct 30.


A Distributed Look-up Architecture for Text Mining Applications using MapReduce.

Balkir AS, Foster I, Rzhetsky A.

Proc Int Symp High Perform Distrib Comput. 2011 Nov;2011. doi: 10.1145/1996130.1996174.


High-resolution coupled physics solvers for analysing fine-scale nuclear reactor design problems.

Mahadevan VS, Merzari E, Tautges T, Jain R, Obabko A, Smith M, Fischer P.

Philos Trans A Math Phys Eng Sci. 2014 Aug 6;372(2021). pii: 20130381. doi: 10.1098/rsta.2013.0381.


On the use of inexact, pruned hardware in atmospheric modelling.

Düben PD, Joven J, Lingamneni A, McNamara H, De Micheli G, Palem KV, Palmer TN.

Philos Trans A Math Phys Eng Sci. 2014 Jun 28;372(2018):20130276. doi: 10.1098/rsta.2013.0276.


The limiting distribution of the effective population size of the ancestor of humans and chimpanzees.

Schrago CG.

J Theor Biol. 2014 Sep 21;357:55-61. doi: 10.1016/j.jtbi.2014.05.009. Epub 2014 May 14.


A MATLAB toolbox for the efficient estimation of the psychometric function using the updated maximum-likelihood adaptive procedure.

Shen Y, Dai W, Richards VM.

Behav Res Methods. 2015 Mar;47(1):13-26. doi: 10.3758/s13428-014-0450-6.


Analyzing large-scale spiking neural data with HRLAnalysis(™).

Thibeault CM, O'Brien MJ, Srinivasa N.

Front Neuroinform. 2014 Mar 5;8:17. doi: 10.3389/fninf.2014.00017. eCollection 2014.


Tool support for software lookup table optimization.

Wilcox C, Strout MM, Bieman JM.

Sci Program. 2011 Dec 5;19(4):213-229.


An efficient, scalable, and adaptable framework for solving generic systems of level-set PDEs.

Mosaliganti KR, Gelas A, Megason SG.

Front Neuroinform. 2013 Dec 26;7:35. doi: 10.3389/fninf.2013.00035. eCollection 2013.


Optimization strategies for fast detection of positive selection on phylogenetic trees.

Valle M, Schabauer H, Pacher C, Stockinger H, Stamatakis A, Robinson-Rechavi M, Salamin N.

Bioinformatics. 2014 Jan 23. [Epub ahead of print]


A Multi-Core Parallelization Strategy for Statistical Significance Testing in Learning Classifier Systems.

Rudd J, Moore JH, Urbanowicz RJ.

Evol Intell. 2013 Nov;6(2). doi: 10.1007/s12065-013-0092-0.


zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm.

Sand A, Kristiansen M, Pedersen CN, Mailund T.

BMC Bioinformatics. 2013 Nov 22;14:339. doi: 10.1186/1471-2105-14-339.


DrML: probabilistic modeling of gene duplications.

Górecki P, Eulenstein O.

J Comput Biol. 2014 Jan;21(1):89-98. doi: 10.1089/cmb.2013.0078. Epub 2013 Sep 27.


A scripted control system for autonomous hardware-timed experiments.

Starkey PT, Billington CJ, Johnstone SP, Jasperse M, Helmerson K, Turner LD, Anderson RP.

Rev Sci Instrum. 2013 Aug;84(8):085111. doi: 10.1063/1.4817213.

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