4Pipe4 – A 454 data analysis pipeline for SNP detection in datasets with no reference sequence or strain information by Pina-Martins, Francisco, Vieira, Bruno M., Seabra, Sofia G., Batista, Dora, Paulo, Octávio S.

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ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences by Yang, Wentao, Rosenstiel, Philip C., Schulenburg, Hinrich

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ADEPT, a dynamic next generation sequencing data error-detection program with trimming by Feng, Shihai, Lo, Chien-Chi, Li, Po-E, Chain, Patrick S. G.

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ADSBET2: Automated Determination of Salt-Bridge Energy-Terms version 2 by Nayek, Arnab, Gupta, Parth Sarthi Sen, Banerjee, Shyamashree, Sur, Vishma Pratap, Seth, Pratyay, Das, Sunit, Islam, Rifat Nawaz Ul, Bandyopadhyay, Amal Kumar

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Advanced SPARQL querying in small molecule databases by Galgonek, Jakub, Hurt, Tomáš, Michlíková, Vendula, Onderka, Petr, Schwarz, Jan, Vondrášek, Jiří

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affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling by Hernandez-Ferrer, Carles, Quintela Garcia, Ines, Danielski, Katharina, Carracedo, Ángel, Pérez-Jurado, Luis A., González, Juan R.

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AFLPsim: an R package to simulate and detect dominant markers under selection in hybridizing populations by Balao, Francisco, García-Castaño, Juan Luis

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AISO: Annotation of Image Segments with Ontologies by Lingutla, Nikhil Tej, Preece, Justin, Todorovic, Sinisa, Cooper, Laurel, Moore, Laura, Jaiswal, Pankaj

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ALDsuite: Dense marker MALD using principal components of ancestral linkage disequilibrium by Johnson, Randall C, Nelson, George W, Zagury, Jean-Francois, Winkler, Cheryl A

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Alignment-free clustering of transcription factor binding motifs using a genetic-k-medoids approach by Broin, Pilib Ó, Smith, Terry J, Golden, Aaron AJ

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AlignWise: a tool for identifying protein-coding sequence and correcting frame-shifts by Evans, Teri, Loose, Matthew

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AllelicImbalance: an R/ bioconductor package for detecting, managing, and visualizing allele expression imbalance data from RNA sequencing by Gådin, Jesper R., van’t Hooft, Ferdinand M., Eriksson, Per, Folkersen, Lasse

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antaRNA – Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization by Kleinkauf, Robert, Houwaart, Torsten, Backofen, Rolf, Mann, Martin

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APP: an Automated Proteomics Pipeline for the analysis of mass spectrometry data based on multiple open access tools by Malm, Erik K, Srivastava, Vaibhav, Sundqvist, Gustav, Bulone, Vincent

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Arabidopsis Motif Scanner by Mele, Giovanni

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Aro: a machine learning approach to identifying single molecules and estimating classification error in fluorescence microscopy images by Wu, Allison Chia-Yi, Rifkin, Scott A

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ASEQ: fast allele-specific studies from next-generation sequencing data by Romanel, Alessandro, Lago, Sara, Prandi, Davide, Sboner, Andrea, Demichelis, Francesca

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ATGme: Open-source web application for rare codon identification and custom DNA sequence optimization by Daniel, Edward, Onwukwe, Goodluck U., Wierenga, Rik K., Quaggin, Susan E., Vainio, Seppo J., Krause, Mirja

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Atom-Atom-Path similarity and Sphere Exclusion clustering: tools for prioritizing fragment hits by Gobbi, Alberto, Giannetti, Anthony M, Chen, Huifen, Lee, Man-Ling

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AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules by Ionescu, Crina-Maria, Sehnal, David, Falginella, Francesco L., Pant, Purbaj, Pravda, Lukáš, Bouchal, Tomáš, Svobodová Vařeková, Radka, Geidl, Stanislav, Koča, Jaroslav

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