Results for "fast"

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  • CNIDARIA: fast, reference-free phylogenomic clustering

    Motivation: Identification of biological specimens is a major requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but these do not scale to arbitrarily large genomes and arbitrarily large phylogenetic distances. ...

    Tags: Bioinformatics, CNIDARIA, Fast, Reference-free, Phylogenomic, Clustering, NGS

    549 days ago

  • FSA: Fast Statistical Alignment

    FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences. Much as distance-based phylogenetic reconstruction methods like Neighbor-Joining build a phylogeny using only pairwise divergence estimates, FS...

    Tags: Bioinformatics, FSA, Fast, Statistical, Alignment, DNA, Sequence

    315 days ago

  • FOGSAA: Fast Optimal Global Sequence Alignment Algorithm

    Sequence alignment algorithms are widely used to infer similarirty and the point of differences between pair of sequences. FOGSAA is a fast Global alignment algorithm. It is basically a branch and bound approach which starts branch expansion in a greedy way taking the symbols from the given pair ...

    Tags: FOGSAA, Fast, Optimal, Global, Sequence, Alignment, Algorithm

    9 days ago

  • PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool

    PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms. Relying on unique software architecture, PLAST takes full advantage of recent multi-core...

    Tags: PLAST, fast, accurate, NGS, scalable, bank-to-bank, sequence, similarity, search, tool

    17 days ago

  • MashMap: a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s)

    MashMap is a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s). It maps a query sequence against a reference region if and only if its estimated alignment identity is above a specified threshold. It does not compute the alignments explicitly, but...

    Tags: MashMap, fast, approximate, software, mapping, long, reads, PacBio, ONT, assembly, reference, genome(s)

    5 days ago

  • Mash: fast genome and metagenome distance estimation using MinHash

    Mash is normally distributed as a dependency-free binary for Linux or OSX (see https://github.com/marbl/Mash/releases). This source distribution is intended for other operating systems or for development. Mash requires c++11 to build, which is available in and GCC >= 4.8 and OSX >= 10....

    Tags: Mash, fast, genome, metagenome, distance, estimation, MinHash

    5 days ago