Search Results for "alignment"
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100 programs for "alignment" with 1 filter applied:
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PFAAT is a Java-based multiple sequence alignment editor and viewer designed for protein family analysis. You can download PFAAT from http://pfaat.sourceforge.net/
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SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAMtools provide efficient utilities on manipulating alignments in the SAM format. The main samtools source code repository moved to GitHub in March 2012. For ongoing development since then, see http://github.com/samtools/samtools
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Subread
High-performance read alignment, quantification and mutation discovery
The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner, Subjunc exon-exon junction detector and featureCounts read summarization program. Subread aligner can be used to align both gDNA-seq and RNA-seq reads. Subjunc aligner was specified designed for the detection of exon-exon junction. For the mapping of RNA-seq reads, Subread performs local alignments and Subjunc performs global alignments. Subread and Subjunc were published in... -
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MView
Extract and reformat a sequence database search or multiple alignment
NOTE: The MView repository and web pages have moved to: https://github.com/desmid/mview https://desmid.github.io/mview/ Release tarballs will continue to be uploaded to SourceForge. ---- MView is a command line utility that extracts and reformats the results of a sequence database search or a multiple alignment, optionally adding HTML markup for web page layout. It can also be used as a filter to extract and convert searches or alignments to common formats. Inputs... -
Small Business HR Management SoftwareWorkforceHub is the instantly useful, delightfully simple to use, small business solution for tracking time, scheduling and hiring. It scales as your business grows while delivering the mission-critical features an organization needs. It is tailored to, built for, and priced for small business employers.
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SimpleXlsxWriter
C++ library for creating XLSX files for MS Excel 2007 and above.
This library represents XLSX files writer for Microsoft Excel 2007 and above. The main feature of this library is that it uses C++ standard file streams. On the one hand it results in almost unnoticeable memory and CPU resources consumption while processing (that may be very useful at saving a large data arrays), but on the other hand it makes unfeasible to edit data that were written. Hence, if using this library the structure of the future report should be known enough. The library... -
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EqmodGui
User interface for INDI Eqmod telescope driver
Eqmodgui is a user interface for Linux INDI Eqmod telescope driver. It allow to easily set the main parameters require to use this driver and manage the alignment data. Eqmod is now very simple to use on Linux. This software is part of a full suite for astronomical observation: https://sourceforge.net/projects/skychart/ https://sourceforge.net/projects/ccdciel/ https://sourceforge.net/projects/indistarter/ See also: https://sourceforge.net/projects/indi/ -
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Tokenized Text Aligner
Aligns tokens in two versions of a text with differing tokenization.
This tool performs token-by-token alignment of two versions of a text with differing tokenization by interpreting the results of a file diff (https://docs.python.org/3/library/difflib.html). It is intended for use in the preparation of annotated linguistic corpora, where differences in tokenization may arise (i) following corrections or modifications to the source text or (ii) through the creation of different layers of annotation (part-of-speech, treebank) requiring different tokenization... -
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PortMedia was created to develop and share cross-platform, open-source I/O libraries for digital media including MIDI, video, and audio. Only a few things were released under the PortMedia umbrella. These are now hosted by the github.com/Portmidi/ project, where you can find the lastest versions of PortMidi, portsmf (Standard MIDI File support and more), and see github.com/rbdannenberg/scorealign for MIDI and/or Audio score alignment.
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m6811dis
M6811 Code-Seeking Disassembler
The M6811 Code-Seeking Disassembler is a command-line tool that lets you enter known starting vectors for a given code image for the 6811 micro. It will disassemble the code and follow through branches to assist in the separation of code and data. Its companion Fuzzy Function Analyzer uses DNA Sequence Alignment Algorithms to locate similar code in multiple binaries, facilitating reverse-engineering. Originally written to analyze code from GM automotive engine controllers, but is useful... -
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A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.
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Java Text Table Formatter is a Java library that renders tables made of characters. The user add cells and can add format characteristics like predefined/custom table styles, text alignment, abbreviation, column width, border types, colspan, etc.
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2D Statistical Models. Building: shape model, texture model and concatenated appearance model; Fitting: 1D profile ASM, 2D profile ASM, direct local texture constrained(LTC) ASM, basic AAM, ICIA AAM, IAIA AAM, etc.
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SCRAM
Probabilistic Risk Assessment Tool
SCRAM is a free and open source probabilistic risk analysis tool. The tool is under development to include fault tree, event tree, common cause, and other standard analyses. -
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An open-source software aimed at unsupervised molecular alignment
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BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads.
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The Lean Mean C++ Option Parser
A no-dependencies C++ program arguments parser
The Lean Mean C++ Option Parser handles the program arguments (argc, argv). It supports the short and long option formats of getopt(), getopt_long() and getopt_long_only() but has a more convenient interface. It is a freestanding, header-only library with no dependencies, not even libc or STL. It comes with a usage message formatter that supports column alignment and line wrapping, making it ideal for localized messages with different lengths. -
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Gallop
A framework for build smooth asynchronous iOS APP
... interface application, can get a great experience. You can easy to insert local images,web images or UIView object in the text. Easily add click and long press events to the text. Easily draw text frame bouding, drawing the hollow words, sets the text vertical Alignment property, etc Easy to parse the expression in the text, like http(s) link, @ user, # theme #, phone number. Fast to sets the image corner radius property and blur processing, can be processed directly after the image. -
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!!! PTEROS DEVELOPMENT MOVED TO GITHUB !!! New project page: https://github.com/yesint/pteros New documentation page: https://yesint.github.io/pteros/ Pteros is the C++ library for custom molecular modeling and simulations codes designed for researchers, not for C++ gurus. Provides facilities for PDB, XTC and TRR files IO, powerful selections, geometry transformations, RMSD fitting and alignment, etc.
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AKtoolbox
Matlab Toolbox for coevolution analysis of multiple sequence alignment
AK Toolbox is a Matlab Toolbox for co-evolution analysis for protein Multiple Sequence Alignment (MSA) distributed under Simplified BSD License. The aim of AK toolbox is to provide a set of Matlab functions, which are independent of Matlab Bioinforamtics Toolbox, for coevolution anaylsis for MSA. At present, co-evolution methods available in this package are Statistical Coupling Analysis (SCA), Explicit Likelihood of Subset Covariance (ELSC), Mutual Information (MI), Observed Minus Expected... -
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SPANDx
Comparative analysis of haploid next-generation genome sequence data
SPANDx is your one-stop tool for identifying SNP and indel variants in haploid genomes using NGS data. SPANDx performs alignment of raw NGS reads against your chosen reference genome or pan-genome, followed by accurate variant calling and annotation, and locus presence/absence determination. SPANDx produces SNP and indel matrices for downstream phylogenetic analyses. Annotated, genome-wide SNPs and indels can also be identified if specified, and are output in human readable format... -
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The Maltcms - Modular Application Toolkit for Chromatography Mass-Spectrometry is a JAVA API for preprocessing, alignment, analysis and visualization of data stored in open file formats used in Proteomics and Metabolomics research.
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converts a SAM file to fasta file. SAM file is a file output from bwa alignment software. It outputs aligned fasta file.
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memstruct
Java library for assembly structures manipulation
MemStruct is a Java library that provides a simple implementation of a basic assembly structure, in order to manipulate and access labelled fields at low-level. MemStruct instances are defined by means of strings. The structure definition syntax is quite similar to what we usually see in macro assemblers. MemStruct supports byte, word, int, short, long and string data, and provides full control of pad bytes, big-endian and little-endian field alignment. -
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PolyRec
Unistroke gesture recognizer
... polylines are aligned to obtain an equal number of segments from both of them; - lastly, the distance is found by summing the contribution of each pair of segments. This implementation is a prototype developed for scientific purposes. More technical details on PolyRec can be found in the following scientific paper: V Fuccella, G. Costagliola; Unistroke Gesture Recognition Through Polyline Approximation and Alignment; in Proceedings of CHI 2015; pp. 3351-3354 http://dl.acm.org/citation.cfm?id=2702 -
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CUSHAW3 is an open-source parallelized, sensitive and accurate short-read aligner. This aligner proposes a general approach to properly aligning both easy and hard reads to large genomes such as the human genome. Perform evaluation on alignment quality reals that CUSHAW3 consistently outperforms CUSHAW2, BWA-MEM, Bowtie2 and GEM in terms of single-end and paired-end alignment. Furthermore, our aligner has demonstrated better paired-end alignment performance than Novalign3 for short-reads...