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  2. GeneMark - Wikipedia

    en.wikipedia.org/wiki/GeneMark

    GeneMark is a generic name for a family of ab initio gene prediction algorithms and software programs developed at the Georgia Institute of Technology in Atlanta.Developed in 1993, original GeneMark was used in 1995 as a primary gene prediction tool for annotation of the first completely sequenced bacterial genome of Haemophilus influenzae, and in 1996 for the first archaeal genome of ...

  3. List of open-source bioinformatics software - Wikipedia

    en.wikipedia.org/wiki/List_of_open-source...

    Linux, macOS, Windows: Common Public 1.0 GenoViz Integrated Genome Browser: Java-based desktop genome browser: Linux, macOS, Windows: Common Public 1.0 GenoViz InterMine: Extensive data warehouse system for the analysis and integration of biological datasets written in Java and JavaScript Cross-platform: LGPL: University of Cambridge: LabKey Server

  4. List of gene prediction software - Wikipedia

    en.wikipedia.org/wiki/List_of_gene_prediction...

    Its name stands for Prokaryotic Dynamic Programming Genefinding Algorithm. It is based on log-likelihood functions and does not use Hidden or Interpolated Markov Models. Prokaryotes, Metagenomes (metaProdigal) [4] AUGUSTUS: Eukaryote gene predictor: Eukaryotes [5] BGF Hidden Markov model (HMM) and dynamic programming based ab initio gene ...

  5. Gene prediction - Wikipedia

    en.wikipedia.org/wiki/Gene_prediction

    Ab Initio gene prediction is an intrinsic method based on gene content and signal detection. Because of the inherent expense and difficulty in obtaining extrinsic evidence for many genes, it is also necessary to resort to ab initio gene finding, in which the genomic DNA sequence alone is systematically searched for certain tell-tale signs of protein-coding genes.

  6. MAFFT - Wikipedia

    en.wikipedia.org/wiki/MAFFT

    O(N^2L) [10] is the time complexity for the guide tree construction, where N is the number of sequences. Progressive Alignment – Using the guide tree progressive alignment [9] is performed from the leaves to the root. The algorithm uses the inputted sequences and aligns the child nodes to calculate a consensus alignment for the parent node.

  7. GLIMMER - Wikipedia

    en.wikipedia.org/wiki/GLIMMER

    GLIMMER was the first system that used the interpolated Markov model [2] to identify coding regions. The GLIMMER software is open source and is maintained by Steven Salzberg , Art Delcher, and their colleagues at the Center for Computational Biology [ 3 ] at Johns Hopkins University .

  8. List of compilers - Wikipedia

    en.wikipedia.org/wiki/List_of_compilers

    Edison Design Group: provides production-quality front end compilers for C, C++, and Java (a number of the compilers listed on this page use front end source code from Edison Design Group [111]). Additionally, Edison Design Group makes their proprietary software available for research uses.

  9. SystemC - Wikipedia

    en.wikipedia.org/wiki/SystemC

    SystemC is a set of C++ classes and macros which provide an event-driven simulation interface (see also discrete event simulation).These facilities enable a designer to simulate concurrent processes, each described using plain C++ syntax.