Search Results for "alignment" - Page 2
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Showing 45 open source projects for "alignment"
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SmithWaterman
Fast local sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align An implementation of the Smith-Waterman local sequence alignment algorithm. See our sister project global alignment using Needleman-Wunsch: http://sourceforge.net/projects/needlemanwunsch/ -
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Fast Alignment Search Tool for di-base reads (color-space; AB SOLiD). A complementary program for the popular Illumina read mappers mrFAST and mrsFAST.
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FFP (Feature frequency profile) is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison.
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gfmessage is a gtk2 based on screen message displayer which prints formatted text on screen. The text can be formatted either using format options such like font , alignment or color options or using the PANGO markup language in input text.
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MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.
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ZORRO is a probabilistic masking program that assigns confidence scores to each column in a multiple seqeunce alignment. These scores can then be used to account for alignment accuracy in phylogenetic inference pipelines.
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BFAST facilitates the fast and accurate mapping of short reads to reference sequences, where mapping billions of short reads with variants is of utmost importance.
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pMap is an MPI-based tool to parallelize the alignment step of state-of-the-art sequence mapping programs. It allows transparent execution of the alignment step of a selected program in parallel on a compute-cluster.
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This software is developed by Kalidas (http://openwetware.org/wiki/Kalidas_Y) as part of his Ph.D. thesis. The method enables alignment of ligand molecules considered molecular graphs. It is useful in the domain of drug discovery and bioinformatics.
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The DNA Sequence Read Toolkit is a set of programs to convert data from DNA sequencing instruments into formats suitable for archiving, viewing or for onward processing (for example alignment or assembly).
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RADAR stands for Rapid Automatic Detection and Alignment of Repeats in protein sequences. RADAR identifies gapped approximate repeats and complex repeat architectures involving many different types of repeats. Radar has moved to github (https://github.com/AndreasHeger/radar)
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An efficient implementation of the Smith-Waterman algorithm that takes advantage of SIMD instruction sets in modern CPUs. The Smith-Waterman algorithm is used for sequence alignment in bioinformatics.
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Xat is named after X-species Alignment Tool. It is designed to be a cross-species cDNA-to-genome alignment software. It is fast and accurate, and optimized for genome-wide mapping.
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aln2dist is a standalone program that uses a multiple sequence alignment to calculate a set of distance matrices and a set of distance restraints (lower and upper bounds). Also require the pdb structure files of homologous proteins to be used as models.
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POA is Partial Order Alignment, a fast program for multiple sequence alignment in bioinformatics. Its advantages are speed, scalability, sensitivity, and the superior ability to handle branching / indels in the alignment.
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This is the command-line C-Language implementation of the PATOSEQ motif alignment algorithm as presented in (Bioinformatics, 18(8):1091-1101, 2002).
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Tifftool is a high-performance tool to clean scanned documents in preparation for onscreen display or for OCR. Features include skew correction, orientation correction, despeckle, page alignment, split pages and batch processing.
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Parallel version of MUMMER v. 3.14, a genome-level alignment tool used to assemble complete genomes.
