Search Results for "dna sequence analysis"
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Showing 405 open source projects for "dna sequence analysis"
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Discourse Network Analyzer (DNA)
Discourse Network Analyzer (DNA)
The Java software Discourse Network Analyzer (DNA) is a qualitative content analysis tool with network export facilities. You import text files and annotate statements that persons or organizations make, and the program will return network matrices of actors connected by shared concepts. -
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proSeq
ProSeq is a GUI program to edit and analyse DNA polymorphism datasets
ProSeq ('Processor of sequences') is a package including GUI and command line programs to process and analyse DNA polymorphism data. It allows one to open and save sequence data in over a dozen file formats (and convert between these formats). It shows sequence alignments in a graphical window and allows the user to edit, manipulate and analyse sequences in various ways. ProSeq4 includes tools to analyse DNA polymorphism, scan for selection, do PCA and reconstruct phylogenies from sequence or SNP data. ... -
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Evo 2
Genome modeling and design across all domains of life
Evo 2 is a DNA language model system designed for long-context genome modeling and biological sequence design across all domains of life. The project models DNA at single-nucleotide resolution and supports context windows of up to one million base pairs, which places it in a class of models built for very large genomic reasoning tasks. According to the repository, it uses the StripedHyena 2 architecture, was pretrained with Savanna, and was trained autoregressively on the OpenGenome2 dataset containing 8.8 trillion tokens. ... -
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XLibraryDisplay
A sequence analysis tool for protein engineering
XLibraryDisplay is an intuitive sequence analysis program optimized for protein engineering. It is ideal for all directed evolution platforms including phage, ribosome, and yeast display. Analysis can be quickly done on hundreds to thousands of sequences. Best suited for Sanger sequencing. Requirements: Microsoft Windows XP, 7, 8, or 10 and Excel 2007, 2010, 2013, or 2016 Described in Stafford et al JCIM 2014: http://pubs.acs.org/doi/abs/10.1021/ci500362s -
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doccano
Open source annotation tool for machine learning practitioners
doccano is an open-source text annotation tool for humans. It provides annotation features for text classification, sequence labeling and sequence-to-sequence tasks. So, you can create labeled data for sentiment analysis, named entity recognition, text summarization and so on. Just create a project, upload data and start annotating. You can build a dataset in hours. -
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binocular
Binocular segmentation of whole-genome DNA sequence data
Segmentation-based detection of copy-number alterations and allelic imbalances in whole-genome DNA sequence data. -
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Bowtie 2
A fast and sensitive gapped read aligner
...Bowtie 2 outputs alignments in SAM format and includes companion utilities for building and inspecting indexes. It is widely used in bioinformatics pipelines for RNA-seq, DNA-seq, metagenomics, variant analysis, and other sequencing-based research tasks. Overall, Bowtie 2 remains a foundational command-line tool for high-throughput sequence alignment and reproducible computational biology workflows. -
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Plaso
Super timeline all the things
Plaso (Plaso Langar Að Safna Öllu), or "super timeline all the things," is a Python-based engine designed for automatic creation of timelines in digital forensic investigations. It processes various log files and artifacts to generate a chronological sequence of events, aiding analysts in understanding system activities. -
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DeepVariant
DeepVariant is an analysis pipeline that uses a deep neural networks
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file. -
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Skill Recorder
Desktop app that records your on-screen work session
...It captures screen activity, clicks, application changes, visited pages, and optional spoken narration while a user performs a task. GitHub Copilot CLI analyzes the recording and reconstructs the overall intent plus an ordered sequence of steps. Users can review and edit that analysis before generating a reusable Skill or scheduled Automation. The generated procedure prefers native agent tools over blindly replaying interface clicks, allowing it to generalize beyond the original demonstration. The application targets macOS primarily, supports Windows 11, and is designed for Microsoft Scout, Copilot Cowork, and Copilot Studio workflows. -
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CpGtools
Python package to analyze DNA methylation data
CpGtools package provides a number of Python programs to annotate, QC, visualize, and analyze DNA methylation data generated from Illumina HumanMethylation450 BeadChip (450K) / MethylationEPIC BeadChip (850K) array or RRBS / WGBS. -
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ESPResSo
The ESPResSo package
...It is designed for coarse-grained and bead-spring models used in physics, chemistry, and molecular biology. The software can model systems such as polymers, colloids, liquid crystals, ferrofluids, DNA, lipid membranes, and other complex fluids. It includes a broad range of interaction potentials and algorithms for electrostatics, hydrodynamics, and coupled particle-field behavior. ESPResSo is controlled through Python, which makes it flexible for custom simulation setup and analysis. Its main value is giving soft matter researchers a versatile and extensible platform for studying many-particle systems beyond simple atomistic models. -
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Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
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ReachabilityAnalysis.jl
Compute reachable states of dynamical systems
Reachability analysis is concerned with computing rigorous approximations of the set of states reachable by a dynamical system. In the scope of this package are systems modeled by continuous or hybrid dynamical systems, where the dynamics change with discrete events. Systems are modeled by ordinary differential equations (ODEs) or semi-discrete partial differential equations (PDEs), with uncertain initial states, uncertain parameters or non-deterministic inputs. -
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Profile Data
Analyze computation-communication overlap in V3/R1
profile-data is a repository that publishes profiling traces and metrics from DeepSeek’s training and inference infrastructure (especially during DeepSeek-V3 / R1 experiments). The profiling data targets insights into computation-communication overlap, pipeline scheduling (e.g. DualPipe), and how MoE / EP / parallelism strategies interact in real systems. The repository contains JSON trace files like train.json, prefill.json, decode.json, and associated assets. Users can load them into tools... -
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This Shiny app provides a user-friendly interface for performing Weighted Gene Co-expression Network Analysis (WGCNA) on RNA-seq/Microarray and DNA methylation (Array/Sequencing) data. It allows for data upload, parameter customization, visualization of results, and exporting of analysis outputs. Online webserver https://shinywgcna.serve.scilifelab.se/app/shinywgcna PLEASE NOTE Datasets with larger dimensions (e.g., 1000x100) may fail on the server,because it is only running on 1GB RAM allocation. ...
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AQUAD
Software for Analysis of Qualitative Data
AQUAD Eight is available in English, German, and Spanish with separate modules for the analysis of texts, audios, videos, graphic files, and a complementary module for exploratory statistical analysis with R. The modules follow the coding paradigm of qualitative analysis, offering for text analysis also functions for sequence analysis (Objective Hermeneutics) and word based quantitative analysis. -
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MAF
Bash Framework to combine many preprocessing and alignment tools
DNA and RNA nucleotide sequences are an ubiquitous element of all biological cells and are serving on one hand as a comprehensive library of capabilities for the cells and on the other as an impressive regulatory system to control cellular function. The presented multi-alignment framework (MAF) should give researchers a simple sequence alignment platform as a functional template, flexible enough to adjust all steps but also comprehensive enough to join many different tools and custom parameter combinations if in-depth analysis is necessary or advised in e.g. low read rate situations. ... -
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MEDe-KIT
Micro Educational and Development Kit (MEDe-KIT)
Micro Educational and Development Kit (MEDe-KIT) is an educational software for storing and viewing information about study material information uploaded to it like images and text descriptions. It uses ODBC for storing uploaded data into local database. Its features also include a genes sequencer for generating combination of DNA and RNA sequence entered. Thanks and hope this is useful for everyone who are interested in science and learning. The project was developed using NetBeans IDE and Java. Default login user name : user Default login password : user -
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janda
structural variant detector
Janda is a tool to detect structural variants in whole-genome DNA sequence data. It identifies structural variants (deletions, duplications, translocations, and inversions) using anomalously mapped pair reads and realigning potential junction reads. -
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ArchCUT3-D
ArchCUT3-D: 3-D Analysis of Incised Archeological Surfaces
Software developed to precisely evaluate the 3-D micromorphological characteristics of archaeological surface incisions. Analysis based on a continuous 3-D slice sequence from a chosen range within the incision path. Measurements and shapes of individual slices can be extracted. ArchCUT3-D’s interface is designed to provide a computational and mathematical analysis of engravings to a wide audience. Please cite Dubinsky, L., David, M., & Grosman, L. (2023). ... -
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UniversalMer2
A CLI k-mer counting tool for multiple size of k at once.
UniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). This kmax can be specified as any length or can be automatically determined by the longest repeated patterns found in the input sequence. -
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NGSEP
NGSEP (Next Generation Sequencing Experience Platform)
NGSEP is an integrated framework for analysis of short and long DNA high throughput sequencing reads. The current version provides functionalities for both de-novo and reference guided analysis of sequencing data, including genome assembly, read mapping, variants detection and genotyping and de-novo analysis of data generated from reduced representation protocols. NGSEP also provides modules for analysis of genomic variation databases (VCF files), including functional annotation, filtering, format conversion, comparison, clustering, imputation, introgression analysis and different kinds of statistics. ... -
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relax
Molecular dynamics by NMR data analysis
The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using anisotropic NMR parameters such as RDCs and PCSs, the investigation of stereochemistry in dynamic ensembles, and the analysis of relaxation dispersion data. -
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MetaEntropy
R package for Virome Mutational Analysis
Estimates Shannon entropy, per gene and per genomic position, associated with non-synonymous mutation frequencies in viral populations, such as wastewater samples. The package uses codon translations for functional insights. Each amino acid can be treated as an individual state, resulting in a 20-state entropy computation, or grouped into one of six physicochemical classes, adding further functional context. Provides normalized values (0-1 scale) to facilitate the direct comparison of...
