Search Results for "alignment" - Page 18
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Showing 492 open source projects for "alignment"
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Protein ALignment Optimiser (PALO) is a script for the selection and alignment of the best combination of transcripts among orthologous genes. PALO is mainly written in Python, although other programming languages are also implemented (R, Perl...).
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MSA2SNP is a tool for mining SNP sites in multiple sequence alignment (MSA). This tool inherits the easy-to-use interface from MEGA4 Explorer with advance data presentation. MSA2SNP lets you visualize alignments and import from CLUSTAL program directly.
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3D Genome Tuner draws circular genome map and enables viewing multi-genomes in 3D context. It also provides genome analysis and sequence alignment, making it a powerful tool in genome studies and demonstrations.
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A peak caller for ChIP-Seq experiments that robustly handles short reads with *multiple* possible mappings. Releases are hosted here, but development source code is available at https://github.com/jakebiesinger/AREM. A Google group has been set up to help with questions from the community and for announcements of new builds. http://groups.google.com/group/arem-announcements
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BoulderALE is an RNA alignment editor, which allows for the annotation of basepairs, annotation and collapsing of features (horizontal) and sequences (vertical), along with 2D display of sequences and base composition given a secondary structure.
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Offers tools to easily manage windows, including automatic alignment and sizing, pinning and unpinning (set on top), shortcuts to stack and view side by side and shortcuts to change size and position.
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Windows command line utility calculating protein orthologs using best reciprocal hit from BLAST alignment output
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Ordered Bijective Interpolated Warping (OBI-Warp) aligns matrices using Dynamic Time Warping with a one-to-one (bijective) smooth warp-function. It is ideal for the chromatographic alignment of complex mass spectrometry proteomics data.
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C++ library for protein sequence profile to profile alignment. Implementing numerous known alignment variants in a flexible and manageable architecture.
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The CMASA (Contact MAtrix based local Structural Alignment algorithm) were used in detecting local protein structural similarity. And it can be applied to enzyme catalytic site annotation. Also visit: http://159.226.149.45/other1/CMASA/CMASA.htm
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Align parallel data at sentence level and also automatic creation of .tmx files for use with Autshumato ITE
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Image and video acquisition for scientific applications, particularly in behavioral biology and neuroscience
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BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC. Annotates the locations of conserved elements in multiple sequence while correcting for alignment uncertainty and error.
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Multi-functional batch sequence aligner incorporating Needleman-Wunsch, Smith-Waterman and Oommen-Kashyap algorithms along with compound alignment of secondary sequences.
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sigMan is a utility for the analysis of time-dependent signals, especially electropherogram/chromatogram data. It is no longer being actively updated or maintained by me (Nathan Cermak) as of January 2011, for lack of any users.
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Optical ray tracing library based on MATLAB environment Now working on the simple raytracing simulation. Documents are not ready yet. NEW UPDATE : ray generation function, other bug fix and multiple ray treatment
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GOALS is a very flexible, adaptable and powerful tool for prototyping and/or building ontology alignment systems. Reusability of existing matching techniques is encouraged. More details at http://www.dei.isep.ipp.pt/~pmaio/goals.
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Sanchay is a collection of tools and APIs for language researchers. It has some implementations of NLP algorithms, some flexible APIs, several user friendly annotation interfaces and Sanchay Query Language for language resources.
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This is an global sequence alignment tool (GSA) created using visual basic 6.0. In this software, Needleman & Wunsch algorithm is used.
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WriteOn is a advanced notepad program that easily allows you to edit and work with several formats of word documents.