“…CONCLUSIONS: Pplacer enables efficient phylogenetic placement and subsequent visualization, making likelihood-based phylogenetics methodology practical for large collections of reads; it is freely available as source code, binaries, and a web service.…”
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“…The sparsification approach yields a significant speed-up in generating predictions, and we demonstrate that the amino acid correlations identified by the algorithm correspond to several known features of protein secondary structure. Datasets and source code used in this study are available at http://noble.gs.washington.edu/proj/pssp.…”
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“…CONCLUSIONS: Based on experimental results, we argue that miRFam is suitable for application as an automated method of family classification, and it is an important supplementary tool to the existing alignment-based small non-coding RNA (sncRNA) classification methods, since it only requires primary sequence information. AVAILABILITY: The source code of miRFam, written in C++, is freely and publicly available at: http://admis.fudan.edu.cn/projects/miRFam.htm.…”
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“…These results demonstrate that our approach allows us to provide clearer principles behind gene regulation mechanisms under histone modifications and detect GHUs further by applying to other microarray and ChIP-chip datasets. The source code of our method, which was implemented in MATLAB (http://www.mathworks.com/), is available from the supporting page for this paper: http://www.bic.kyoto-u.ac.jp/pathway/natsume/hm_detector.htm.…”
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“…FINDINGS: We present modified C++ source code for the EvolSimulator platform, which we provide as the extension module NU-IN. …”
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“…CONCLUSIONS: FluReF demonstrates robustness of prediction for geographically and temporally expanded datasets, and is not limited to finding reassortments with previously collected sequences. The complete source code is available from http://lcbb.epfl.ch/software.html.…”
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“…Alternatively, FC can be compiled from the source code on any Unix machine and then run with the possibility of customizing each single parameter through a simple configuration text file that can be generated using a dedicated user-friendly web-form. …”
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“…The results of CLASP analysis on motifs extracted from Catalytic Site Atlas (CSA) are also presented in order to demonstrate its ability to accurately classify any protein, putative or otherwise, with known structure. The source code and database is made available at www.sanchak.com/clasp/. …”
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“…We make our program available as downloadable source code, and as a plugin for a genome browser installed on our servers.…”
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“…Availability: The program deepBlockAlign is available as source code from http://rth.dk/resources/dba/. Contact: gorodkin@rth.dk; studla@bioinf.uni-leipzig.de Supplementary information: Supplementary data are available at Bioinformatics online.…”
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“…CONCLUSIONS: ABrowse framework is valuable for end users, data providers and developers by providing rich user functions and flexible customization approaches. The source code is published under GNU Lesser General Public License v3.0 and is accessible at http://www.abrowse.org/. …”
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“…CONCLUSIONS: Both DISCO-SCA and properly applied GSVD are promising integrative methods for finding common and distinctive processes in multisource data. Open source code for both methods is provided.…”
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“…By providing the ability to identify novel candidate genes in model organisms, our method opens the door to new models for studying diseases. Availability: Source code and supplementary information is available at: www.andrew.cmu.edu/user/aaronwis/cotrain12. …”
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“…The software iNA is freely available as executable binaries for Linux, MacOSX and Microsoft Windows, as well as the full source code under an open source license.…”
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“…Detailed results for single machine learning methods and the consensus methodology are also provided, together with the comparison to previously published methods and state-of-the-art software tools. The source code and precompiled binaries of brainstorming tool are available at http://code.google.com/p/automotifserver/ under Apache 2.0 licensing. …”
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“…AVAILABILITY AND IMPLEMENTATION: SS-CoSBI is implemented in C. The source code is freely available at http://www.healthcare.uiowa.edu/labs/tan/SS-CoSBI.gz.…”
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“…For reproducibility and future work we provide R source code for all calculations.…”
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“…CONCLUSIONS: Fusion of mRNA and miRNA expression data into one prediction model improves clinical outcome prediction in terms of prediction error and stable feature selection. The R source code of the proposed method is available in the supplement.…”
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“…Likewise, substantial filtering was performed on bacterial RNA–RNA interaction data. Availability: The source code for RIsearch is available at: http://rth.dk/resources/risearch. …”
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“…Additionally, simulations also indicate that the probability of incorrectly identifying a protein as differentially expressed (i.e., the False Discovery Rate) is very low. The source code is available at https://github.com/stevenhwu/BIDE-2D.…”
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