Results for "AligNment"

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  • progressiveCactus

    Progressive Cactus is a whole-genome alignment package. Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules https://github.com/glennhickey/progressiveCactus

    Tags: Progressive, Cactus, Whole-genome, Alignment, Package, progressiveCactus

    2506 days ago

  • maf2synteny

    A tool for converting for recovering synteny blocks from multiple alignment (in MAF fromat) This tool is a standalone version of Ragout module [http://fenderglass.github./Ragout]

    Tags: Tool, Conversion, Recover, Synteny, Blocks, Multiple, Alignment, MAF, Format, maf2synteny

    2506 days ago

  • AVID: A Global Alignment Program

    A new global alignment method called AVID. The method is designed to be fast, memory efficient, and practical for sequence alignments of large genomic regions up to megabases long. We present numerous applications of the method, ranging from the comparison of assemblies to alignment of large synt...

    Tags: AVID, Global, Alignment, Program

    2500 days ago

  • SIMA C++ Implementation: Simultaneous Multiple Alignment of LC/MS Peak Lists

    This is the c++ implementation for SIMA - Simultaneous Multiple Alignment of LC/MS Peak Lists. The package contains C++ source code as well as two binary files. The latter were tested under various operating systems, including Windows XP SP3 32bit, Windows Vista 32bit, Windows 2008 Server, Window...

    Tags: SIMA, C++, Simultaneous, Multiple, Alignment, LC/MS, Peak, Lists

    2317 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

    2302 days ago

  • CrusView

    CrusView is a java based tool for karyotype/genome visualization and comparison of crucifer Species. It also integrates an binary version of KGBassembler and a post-modification step for its assembling result.

    Tags: CrusView, Plant, View, Visualization, See, Alignment

    2177 days ago

  • BlasR Mapping single molecule sequencing reads using Basic Local Alignment with Successive Refinement (BLASR): Theory and Application,

    BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion error. Here is how I use the blasr to align PacBio rea...

    Tags: Mapping, single, molecule, sequencing, reads, Basic, Local, Alignment, Successive, Refinement, BLASR

    2136 days ago

  • LSC: Improving PacBio Long Read Accuracy by Short Read Alignment

    Added Command line argument support. Multi-stage execution modes. Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set by --long_read_batch_size N. Better compressed intermediate files. Added utilities folder. Added support for multiple ...

    Tags: LSC, Improve, correct, PacBio, Long, Read, Accuracy, Short, Read, Alignment

    2030 days ago

  • lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data

    lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads and application. lordFAST, a novel long-read mapp...

    Tags: lordFAST, sensitive, Fast, Alignment, Search, Tool, LOng, noisy, Read, sequencing, Data

    1948 days ago

  • MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

    MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupt...

    Tags: MACSE, Multiple, Alignment, Coding, SEquences, Accounting, Frameshifts, Stop, Codons

    1865 days ago