Search Results for "multiple sequence alignment" - Page 3
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Showing 311 open source projects for "multiple sequence alignment"
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SmartRulerCapture
Professional screen capture tool with built‑in rulers multi-capture
Smart Ruler Capture is a professional screen capture tool designed for designers, developers, and anyone needing precise on‑screen measurements. It features multiple active capture zones, an overlay ruler with configurable units (px, in, cm), and a customizable grid for perfect alignment. The app offers eight color themes, full keyboard control, and works entirely offline - no analytics, no cloud uploads. Settings are automatically saved between sessions. Includes handy keyboard shortcuts like Capture Commands -- Ctrl+Shift+C - Capture all visible areas -- Ctrl+Alt+C - Capture active area only -- Ctrl+Shift+F - Full screen capture Area Manipulation -- Ctrl+Arrows - Resize active area -- Ctrl+V - Paste from Clipboard -- Ctrl+Alt+V - Vertical Ruler -- Ctrl+Alt+H - Horizontal Ruler -- Ctrl+Alt+O - Toggle Ruler Available as an installer or portable version for Windows. ... -
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comer2
COMER2, cross-platform software for protein remote homology search
The COMER method based on sequence profile-profile comparison is one of the most sensitive and accurate computational tools developed for protein alignment and homology search. COMER version 2.1 (COMER2) represents one of the fastest implementations of calculations for sensitive protein homology search. High COMER2 performance is achieved by harnessing the power of the Graphics processing unit (GPU). -
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BIGSdb
Software for storing and analysing bacterial sequence data
The Bacterial Isolate Genome Sequence Database (BIGSdb) is a scalable, web-accessible database system designed to store and analyse linked phenotypic and genotypic information in a computationally efficient manner. Sequence data can range from single sequence reads to multiple contigs generated by whole genome sequencing technologies. The system incorporates the capacity to define and identify any number of loci and genetic variants at those loci within the stored nucleotide sequences. ... -
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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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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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OpenNMT-tf
Neural machine translation and sequence learning using TensorFlow
...For example, the following instance defines a sequence-to-sequence model with 2 concatenated input features, a self-attentional encoder, and an attentional RNN decoder sharing its input and output embeddings. Sequence to sequence models can be trained with guided alignment and alignment information are returned as part of the translation API. -
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Iperf 2
A means to measure network responsiveness and throughput
Iperf here is a means of measuring networks - capacity & latency (including ECN) over sockets both TCP and UDP. The goals include maintaining an active iperf code base across a broad set of platforms and operating systems. This is a multi-threaded design that scales with the number of CPUs or cores within a system. It supports both high impact and low impact techniques to obtain and report network performance. Current release: 2.2.1, Nov 4th, 2024 About iperf 2 and iperf3: Read... -
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miRDeep*
MiRDeep*
Please cite: An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013) miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res, 41, 727-737. We will create index for you if you tell us your interested species (j.an@qut.edu.au). download command line version "MDS_command_line_Vxx.zip" clicking "Browse All Files" please find miRPlant in sourceforge for plant miRNA prediction. -
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JDiskMark
Java Disk Benchmark Utility
JDiskMark is a powerful and versatile disk benchmarking tool written in Java, designed to help you accurately measure the performance of your storage devices across different operating systems. Whether you're testing HDDs, SSDs, or network drives, JDiskMark provides reliable insights into your disk's read and write speeds. ubuntu/debian installer: https://sourceforge.net/projects/jdiskmark/files/jdiskmark_0.6.3_amd64.deb/download rhel / fedora... -
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Bit-Twist (Packet generator/editor)
Packet generator and packet editor for Windows, Linux, BSD, and macOS
Supported systems: Windows, Linux, BSD, and macOS. Bit-Twist is a simple yet powerful libpcap-based Ethernet packet generator and packet editor. It is designed to complement tcpdump, which by itself has done a great job at capturing network traffic. With Bit-Twist, you can now regenerate your captured traffic onto a live network! Packets are generated from tcpdump trace file (.pcap file). Bit-Twist comes with a comprehensive trace file editor to allow you to change the contents of a... -
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ReViMS
ReViMS, a 3D volume rendering tool for light-sheet/confocal microscopy
Reconstruction and Visualization from Multiple Sections (ReViMS), an open-source, user-friendly software for automatically estimating volume and several other features of 3D multicellular aggregates (i.e., cancer spheroid, zebrafish, fruit fly). ReViMS requires a z-stack of 2D binary masks, obtained by segmenting a sequence of fluorescent images acquired by scanning the aggregate along the z axis, using a confocal or a light-sheet fluorescent microscope. -
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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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Billiards Covers
This zip jar contains the current coverings of periodic paths.
Researchers, Mathematicians and Enthusiasts. Download "Billiards Covers" to see the most current list of periodic paths in triangles. Download "Billiards Everything" to discover new periodic billiard paths, an unresolved problem from 1775! Follow "The Great Periodic Path Hunt" at gwtokarsky.github.io for the latest news. Email tokarsky@ualberta.ca for feedback. -
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DSL-KeyPad
Multilingual input tool. Latin, Cyrillic, IPA, Math, historic, etc.
“DSL KeyPad” is a utility written on AutoHotkey 2.0, designed for inputting a wide range of characters using hotkeys and auxiliary functions. Its primary focus is on enhancing input capabilities for Latin and Cyrillic scripts, allowing typing in multiple languages without the need for separate keyboard layouts for each language. Requires common QWERTY (English US)/ЙЦУКЕН (Russian) keyboard layouts. More than 6,300 Unicode characters are available. Additionaly, it supports typing on the... -
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kSNP
kSNP4 does SNP discovery and SNP annotation from whole genomes
kSNP4 identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs. SNP discovery is based on k-mer analysis, and requires no multiple sequence alignment or the selection of a reference genome, so kSNP4 can take 100's of microbial genomes as input. A SNP locus is defined by an oligo of length k surrounding a central SNP allele. kSNP4 can analyze both complete (finished) genomes and unfinished genomes in assembled contigs or raw, unassembled reads. Finished and unfinished genomes can be analyzed together, and kSNP can automatically download Genbank files of the finished genomes and incorporate the information in those files into the SNP annotation. ... -
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Metaseq
Repo for external large-scale work
Metaseq is a flexible, high-performance framework for training and serving large-scale sequence models, such as language models, translation systems, and instruction-tuned LLMs. Built on top of PyTorch, it provides distributed training, model sharding, mixed-precision computation, and memory-efficient checkpointing to support models with hundreds of billions of parameters. The framework was used internally at Meta to train models like OPT (Open Pre-trained Transformer) and serves as a... -
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Classroom Insights is a software designed to compute various statistical metrics from a CSV file/database of students' and teachers' performance records. It was intended to be the teacher's companion when drafting end-of-sequence or end-of-year reports on classroom performances after evaluations. This software features multiple tools to provide the teacher with a unique perspective on their students' performances across evaluations. This software makes use of quantitative and graphical methods to provide insights. As a bonus, Classroom Insights is designed to allow for archiving statistics per sequence into a database file that can be shared with other colleagues for a more comprehensive perspective on performance. ...
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Vibrance HDR
Create HDR image effect, from a single or multiple (AEB) photos.
Vibrance HDR is an app for Android(TM), which allows you to create high dynamic range (HDR) images, either from a single photo, or from multiple* auto exposure bracketed (AEB) photos. High-dynamic-range imaging is a technique used in photography to reproduce a greater dynamic range of luminosity. This works best in conjunction with a camera app that supports taking photos at multiple different exposures. However Vibrance HDR also supports creating a "HDR-like" effect from a single... -
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Alphafold
Open source code for AlphaFold
This package provides an implementation of the inference pipeline of AlphaFold v2.0. This is a completely new model that was entered in CASP14 and published in Nature. For simplicity, we refer to this model as AlphaFold throughout the rest of this document. Any publication that discloses findings arising from using this source code or the model parameters should cite the AlphaFold paper. Please also refer to the Supplementary Information for a detailed description of the method. You can use... -
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Fairseq
Facebook AI Research Sequence-to-Sequence Toolkit written in Python
Fairseq(-py) is a sequence modeling toolkit that allows researchers and developers to train custom models for translation, summarization, language modeling and other text generation tasks. We provide reference implementations of various sequence modeling papers. Recent work by Microsoft and Google has shown that data parallel training can be made significantly more efficient by sharding the model parameters and optimizer state across data parallel workers. These ideas are encapsulated in the... -
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SGP AutoFocus LogViewer
Autofocus log viewer for Sequence Generator Pro.
This software extracts relevant autofocus data from the log files generated by the Sequence Generator Pro astrophoto capture software. It further allows to graph all the autofocus runs stored in the logfile and to calculate temperature coefficients and filter offsets. -
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Augmentor.jl
A fast image augmentation library in Julia for machine learning
A fast library for increasing the number of training images by applying various transformations. Augmentor is a real-time image augmentation library designed to render the process of artificial dataset enlargement more convenient, less error prone, and easier to reproduce. It offers the user the ability to build a stochastic image-processing pipeline (or simply augmentation pipeline) using image operations as building blocks. In other words, an augmentation pipeline is little more but a... -
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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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CView
Alignment viewer that incorporates a dynamic graphical network.
> CView wiki: https://sourceforge.net/p/cview/wiki/Home/ Related Software: 1. CStone: https://sourceforge.net/projects/cstone/ 2. CSReadGen: https://sourceforge.net/projects/csreadgen/ 3. CView: (See wiki) 4. ChimSim: https://sourceforge.net/projects/chimsim/ 5. TVScript: https://sourceforge.net/projects/tvscript/ 6. SeQuester: https://sourceforge.net/projects/sequester/ 7. TreeScope: https://sourceforge.net/projects/treescope/ -
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Peptide Pattern Recognition
Software for non-alignment based analysis of DNA and protein sequences
Software for analysis, grouping and functional prediction of DNA and protein sequences as described in: Busk P.K. (2017). Peptide Pattern Recognition for high-throughput protein sequence analysis and clustering. BioRxiv. doi: https://doi.org/10.1101/181917. Busk P.K. and Lange L. (2013). Function-based classification of carbohydrate-active enzymes by recognition of short, conserved peptide motifs. Appl Environ Microbiol. 79(11), 3380-91. Busk P.K. Lange M. Pilgaard B. and Lange L. (2014)....
