Search Results for "multiple sequence alignment"
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Showing 39 open source projects for "multiple sequence alignment"
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Cpp17
Chinese translation of C++17 The Complete Guide
...It also covers enhancements to existing STL components, new library utilities, and advanced topics like polymorphic memory resources (PMR), alignment, and generic programming improvements. -
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Task Scheduler
Cooperative multitasking for Arduino, ESPx, STM32, nRF and more
Cooperative multitasking for Arduino, ESPx, STM32 and other microcontrollers. A lightweight implementation of cooperative multitasking (task scheduling). An easier alternative to preemptive programming and frameworks like FreeRTOS. You mostly do not need to worry about pitfalls of concurrent processing (races, deadlocks, livelocks, resource sharing, etc.). The fact of cooperative processing takes care of such issues by design. -
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gendasm
Generic Code-Seeking Diassembler with Fuzzy-Function Analyzer
...It will disassemble the code and follow through branches to assist in the separation of code and data. Its included Fuzzy Function Analyzer companion uses a DNA Sequence Alignment Algorithm to locate similar code in multiple binaries to facilitate reverse-engineering and/or code recovery. The original purpose of the Fuzzy Function Analyzer was to assist in code recovery where the source code for the current binaries got lost, yet the source code for an old binary was retained. The Fuzzy Function Analyzer allows you to match up known functions between the two binaries so you can concentrate on disassembling and reverse engineering the parts that are different and recover the code for the current binary that got lost. -
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flom
Free Lock Manager
FLoM is a free open source distributed lock manager that can be used to synchronize shell commands, scripts and custom developed software. When used in a shell environment, FLoM manages process synchronization in the same way that "nice" manages process prioritization. Shell commands, scripts and custom programs can be synchronized inside a single system or in a network of IP connected systems. FLoM supports different types of abstract resources: simple, numeric, set, hierarchical and... -
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sRNAWorkbench
The UEA sRNA Workbench
A suite of tools for analysing small RNA (sRNA) data from Next Generation Sequencing devices. Including expression profiling of known mirco RNA (miRNA), identification of novel miRNA in deep-sequencing data and identification of other interesting landmarks within high-throughput genetic data -
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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 anywhere a 6811 micro is being used. Version 1.0 was written in Borland Pascal in April 1996, and updated to v1.2 in June 1999. It was later rewritten to C++ in July 1999 through Jan 2000. ... -
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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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M80AttributedLabel
Another attributed label using CoreText
M80AttributedLabel is a feature-rich UILabel alternative that supports rich text rendering with advanced formatting options. It allows embedding links, images, and custom text styling within a label, supporting complex layouts. -
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LCUI
A small C library for building user interfaces with C, XML and CSS.
LCUI is a freely available software library to create GUI application, it is written in C, support the use XML and CSS describe the graphical interface, you can use it to make some simple effects. The above description and screenshots is for the version 1.0.0 (+), and the 1.0.0 version is still in development, it is not officially released, please do not use old versions of "files "page to download as version 1.0.0. -
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FreeFileSync
Free data backup software to synchronize files and folders
FreeFileSync is a free Open Source software that helps you synchronize files and synchronize folders for Windows, Linux and macOS. It is designed to save your time setting up and running data backups while having nice visual feedback along the way. _______________________________________________________________ DOWNLOAD LINKS (official homepage): https://freefilesync.org/ -
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IPAS for protein sequences
multiple alignment algorithm for protein sequences
IPAS is a new and practial protein multiple sequence alignment algorithm based on iterative progresive alignment algorithm Assessed on BAliBASE 3.0, PREFAB 4.0, SABMARK 1.65, and OXBENCH, MSAProbs achieves the statistically highest alignment accuracy, compared to ClustalW 2.0.10, MAFFT 6.717( using L-INS-i with --maxiterate = 1000), MUSCLE 3.8.31, ProbCons 1.12, and Probalign 1.3. -
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MSAProbs: Multiple Sequence Alignment
One of the most accurate multiple protein sequence aligners
MSAProbs is an open-source protein multiple sequence ailgnment algorithm, achieving the stastistically highest alignment accuracy on popular benchmarks: BALIBASE, PREFAB, SABMARK, OXBENCH, compared to ClustalW, MAFFT, MUSCLE, ProbCons and Probalign. -
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Mauve computes and interactively visualizes genome sequence comparisons. Using FastA or GenBank sequence data, Mauve constructs multiple genome alignments that identify large-scale rearrangement, gene gain, gene loss, indels, and nucleotide substutit
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biosbl
Standard Bioinformatics Library
set of classes used to handle input/outputs of bioinformatics data files and basic operations as multiple alignment and phylogenetic reconstruction. -
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sam_comp
Compression for SAM/BAM file format
This is a simple arithmetic coding based compressor for the SAM and BAM (DNA sequence alignment) file format. -
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RT-alignment
Graph-based time alignment algorithms for multiple LC-MS datasets
...An LC-MS analysis of a complex biological sample can be visualized as a “map” of which the positional coordinates are the mass-to-charge ratio (m/z) and chromatographic retention time (RT) of the chemical species profiled. Label-free quantitative-proteomics requires the alignment and comparison of multiple LC-MS maps to ascertain the reproducibility of experiments or reveal proteome changes under different conditions. The main challenge in this task lies in correcting retention time shifts, which are inevitable even on the same instrument and under the same elution conditions. For large-scale studies, multiple instruments or multi-week experiments are often required, which exacerbates the problem. ... -
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SWAPHI-LS: Alignment on Xeon Phi Cluster
Smith-Waterman long DNA sequence alignment on Xeon Phi clusters
The first parallel Smith-Waterman algorithm exploiting Intel Xeon Phi clusters to accelerate the alignment of long DNA sequences. This algorithm is written in C++ (with a set of SIMD intrinsic extensions), OpenMP and MPI. The performance evaluation revealed that our algorithm achieves very stable performance, and yields a performance of up to 30.1 GCUPS on a single Xeon Phi and up to 111.4 GCUPS on four Xeon Phis sharing a host. -
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qcv
Computer Vision Framework Library (for Linux)
QCV is a Qt-based computer vision framework library that provides an easy to use interface to display, analyze and run computer vision algorithms. The library is provided with practical examples to show what you can do with just a few lines of code. OpenCV is used as the supporting computer vision library. QCV provides interfaces for C and C++. The C interface is a set of simple function calls to allow the user to visualize data and obtain events from the system and user input. The... -
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SWAPHI: Smith-Waterman on Intel Xeon Phi
The first protein sequence database search on shared-host Xeon Phis
The first parallel algorithm to accelerate the Smith-Waterman protein database search on shared-host multiple Intel Xeon Phi coprocessors. By searching against the UniProtKB/TrEMBL database, SWAPHI achieves a performance of up to 58.8 billion cell updates per second (GCUPS) on a single Xeon Phi and up to 228.4 GCUPS on four Xeon Phis. -
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jaivox
Speech recognition application builder and library
Java library and tools to create open source speech recognition applications. Generates dialogs for conversational interfaces. Works with a popular open source speech recognition library. -
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PANDA
Passing Attributes between Networks for Data Assimilation
PANDA (Passing Attributes between Networks for Data Assimilation), is a message-passing model to gene regulatory network reconstruction. PANDA integrates multiple sources of biological data, including protein-protein interaction, gene expression, and sequence motif information, in order to reconstruct genome-wide, condition-specific regulatory networks. PANDA is also available in other programming languages, including: MATLAB/Octave: (1) https://drive.google.com/a/channing.harvard.edu/file/d/0BwVdzX3nIj6RamtmNVdKYVk1N2c/view?... -
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FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.
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MSA-CUDA: multiple sequence aligner
multiple sequence alignment on CUDA-enabled GPUs.
This project is not active any more since we failed to get the permit from the Clustal team to distribute our software. You can refer to the paper "Yongchao Liu, Bertil Schmidt, Douglas L Maskell:MSA-CUDA: multiple sequence alignment on graphics processing units with CUDA. ASAP 2009" for more details. -
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Hierachical_DNAcoder
An Hierachical Approach to Multi-Reference Genome compression
The storage and data transferring of large genome data are becoming important concerns for biomedical researchers. We present a novel multi-reference based genome compression method with a hierachical structure. Our approach works for the de facto standard alignment format (i.e., BAM) compression that is the pressing need at present. We align new sequences to a reference sequence using SOAP3, a GPU-based aligning software, and summarize mapping properties and information for exact mapped reads. To increase the exact aligning rate, we also realign the approximately mapped and unmapped reads by changing the reference sequence or shortening the read length. ... -
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GenNon-h
Simulating non-homogeneous multiple sequence alignments
...Moreover, existing software restricts to the time-reversible models and it is not optimized to generate nonhomogeneous data (i.e. placing distinct substitution rates at different lineages). GenNon-H is the first package designed to generate multiple sequence alignments under the discrete-time Markov processes on phylogenetic trees, which samples directly from the transition matrices. Based on the input model and a phylogenetic tree in the Newick format (with branch lengths measured as the expected number of substitutions per site), the algorithm produces DNA alignments of desired length. ...
