“…In contrast, the multi-threaded original tool needs 2.77 and 5.54 hours to perform the same alignments on the 64 cores of one node. The source code of our parallel implementation is publicly available at the CUSHAW3 homepage (http://cushaw3.sourceforge.net).…”
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“…We recommend that: in practical applications, the layout AoaS is the best choice since the tiled version is the fastest one among three versions. The source code of all implementations are publicly available. …”
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“…Edesign can be freely accessed online at http://www.dnaform.com/edesign2/, and the source code is available for download.…”
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“…We describe here the principles of ROMA providing several practical examples of its use. ROMA source code is available at https://github.com/sysbio-curie/Roma.…”
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“…Availability and implementation: Open source code and documentation are available for download at http://github.com/ratschlab/mmr. …”
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“…Availability and implementation: Software performing thesaurus annotation is implemented in java; available in source code on github at GeneticThesaurus (https://github.com/tkonopka/GeneticThesaurus) and as an executable on sourceforge at geneticthesaurus (https://sourceforge.net/projects/geneticthesaurus). …”
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“…Also, we have released our source code for non-commercial use.…”
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“…Furthermore, our method surpasses three competing methods: MCL, ClusterOne, and MCODE in terms of the quality of the predicted complexes. The source code and accompanying examples are freely available at http://faculty.kfupm.edu.sa/ics/eramadan/GACluster.zip.…”
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“…In this paper we describe the Lollipops software for the presentation of panel or exome sequencing results. Source code and binaries are freely available at https://github.com/pbnjay/lollipops. …”
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“…Moreover, if necessary they can be further developed by users writing their portions of code. The source code, documentation, and wiki, as well as the issue tracker and the list of related articles that use ChroTeMo and ChroTeVi, are accessible in a public repository at Github under GPL 3.0 license.…”
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“…The new deepTools2 suite can be easily deployed within any Galaxy framework via the toolshed repository, and we also provide source code for command line usage under Linux and Mac OS X. …”
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“…Our modified OpenRasmol is distributed following the license, RASLIC, as an open source code at our web site (www.irisa-lab.bio.kyutech.ac.jp/openrasmol), where video files showing rendering speeds of our modified OpenRasmol are also available.…”
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“…GFinisher can easily optimize assemblies of prokaryotic draft genomes and can be used to improve the assembly programs based on nucleotide sequence patterns in the genome. The software and source code are available at http://gfinisher.sourceforge.net/.…”
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“…We used Percolator 3.0 to analyze the data from a recent study of the draft human proteome containing 25 million spectra (PM:24870542). The source code and Ubuntu, Windows, MacOS, and Fedora binary packages are available from http://percolator.ms/ under an Apache 2.0 license. …”
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“…Availability and Implementation: Web application: http://www.heatstarseq.roslin.ed.ac.uk/. Source code: https://github.com/gdevailly. Contact: Guillaume.Devailly@roslin.ed.ac.uk or Anagha.Joshi@roslin.ed.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.…”
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“…Generally, such network topology features provide insights into the relationship between protein functions and network architectures. The source code of Matlab is freely available on request from the authors.…”
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“…This helps us to simulate the SHAPE data for any RNA sequence and consequently improves the accuracy of RNA secondary structure prediction as it is confirmed by our experiments. The source code and web server of our proposed method are freely available at http://mostafa.ut.ac.ir/ESD-Fold/.…”
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“…The comparison with two widely used available tools, namely VarScan and GATK, shows that MICADo is more accurate, especially when true mutations have frequencies close to backgound noise. The source code is available at http://github.com/cbib/MICADo.…”
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“…AVAILABILITY AND IMPLEMENTATION: MPRAnator tool set is implemented in Python, Perl and Javascript and is freely available at www.genomegeek.com and www.sanger.ac.uk/science/tools/mpranator. The source code is available on www.github.com/hemberg-lab/MPRAnator/ under the MIT license. …”
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“…Our results demonstrate that our method can be successfully used to extract relations from literature about a biological process without an annotated corpus. The source code and data used in this study are available at https://github.com/AndreLamurias/IBRel.…”
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