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Free and Open Source Software
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D-GENIES - interactive dot plots for genome comparisons
Dot plots provide a visual representation of sequence similarity between genomes. They are particularly useful for detecting structural differences, including rearrangements, inversions, duplications and regions that fail to align. However, producing useful comparisons can become computationally demanding when working with very large assemblies.
D-GENIES combines genome alignment software with a browser-based visualisation interface. Researchers can examine the results interactively, making it easier to investigate similarities and structural differences between assembled sequences.
This is free and open source software.
Paranoya - IOC and YARA malware scanner
The scanner combines indicators of compromise with YARA rules from several security-focused sources. These include rule collections used for identifying malware families, phishing kits and other suspicious content. Paranoya can therefore use both file characteristics and signature-based rules when assessing material presented for analysis.
Paranoya can also operate as a persistent scanning daemon. An accompanying client submits files or paths to the scanner, allowing it to be integrated into automated security workflows without starting a new scanning process for every request. Listening addresses, ports, output behaviour and logging can be adjusted through command-line options.
An intensive scanning mode enables additional checks when a more thorough examination is needed. The software also provides configurable output and can produce CSV results for further processing. Its rule-based design allows detection coverage to evolve as new YARA signatures and indicators are introduced, while the project continues to receive maintenance and security-related updates.
This is free and open source software.
ch4 - command-line DNS client compatible with dig
The application supports EDNS and lets you control the maximum UDP payload size. Unknown DNS record types can be represented using the generic format specified by RFC 3597, while an option is available to force that representation for all records.
For scripts and other situations where the normal detailed response is unnecessary, ch4 offers short output containing only record data. It can also save DNS responses to a file and read previously saved responses.
Other facilities include configurable query lifetimes and timeouts, a command for listing the nameservers detected from the operating system, and build information describing the version and compilation environment.
ch4 is therefore well suited to users who want a relatively familiar dig-like workflow backed by a modern Rust DNS implementation.
This is free and open source software.
Anime4KCPP - high performance anime upscaler
Hardware acceleration is available through OpenCL and CUDA, while the CPU implementation takes advantage of architecture-specific SIMD instruction sets including SSE, AVX, AVX2, AVX-512, NEON and other platform-specific vector extensions. This gives Anime4KCPP broad hardware support while allowing modern CPUs and GPUs to accelerate demanding enlargement workloads.
Anime4KCPP also offers a video module built on FFmpeg libraries, Python and C bindings, and integration with VapourSynth. A WebAssembly-based playground lets users experiment with the upscaling engine directly in a browser.
This is free and open source software.
IGV-Web App - explore genomic data in a web browser
The application is built around igv.js, which provides the underlying visualisation capabilities. Unlike the embeddable library, IGV-Web App offers a complete interface for researchers who simply want to load genomic data and investigate it.
Data can be loaded from local files or remote sources. When working with local files, the application processes the data in the browser rather than uploading it to the hosting server, an important consideration when handling unpublished research data.
This is free and open source software.
Rebiber - replace unofficial BibTeX entries with official record
The software matches records using title information together with author checks intended to reduce incorrect substitutions. Its packaged publication data covers a broad selection of computer science conferences and journals. An optional live lookup can search DBLP when a suitable record is not available in the local data.
A dry-run mode shows proposed changes without modifying the bibliography, while reports can be written to a separate file. Rebiber can restrict replacements to citation keys actually used by specified TeX files and can process multiple BibTeX files in one operation.
Formatting facilities include retaining only selected fields, removing unwanted fields, protecting acronyms in titles, abbreviating venue names, sorting entries by citation key and controlling duplicate keys. A format-only mode applies formatting without attempting to replace publication records.
This is free and open source software.
Kookbook - recipe manager using structured Markdown files
Its approach separates reading from editing. Kookbook presents recipes in an accessible interface while relying on an external text editor to make changes. This keeps the recipes independent of the application and avoids locking a collection into a specialised database format.
The underlying files can be stored wherever you prefer, making it possible to keep a recipe collection under version control or synchronise it using external services such as Git or Nextcloud.
This is free and open source software.
Best Free and Open Source Alternatives to Microsoft Phone Link
Microsoft Phone Link connects a Windows PC with an Android phone or iPhone. It lets users read and reply to messages, manage phone notifications, make and receive calls, and access recent photos from the desktop. With supported Android devices, additional features include using mobile apps, sharing clipboard content and transferring files.
Phone Link is proprietary software and is not available for Linux. There is no exact open source replacement covering every feature, but there are some excellent alternatives.
Journaler - Privacy-Focused Daily Journaling App
Journaler includes global search for finding words or phrases across the journal and can jump directly to the corresponding day. Writing statistics provide information such as word counts, writing activity and streaks. There is also a focus mode intended to reduce distractions while writing, together with light and dark themes.
The application can export the complete journal as a ZIP archive and provides facilities for printing either an individual entry or the whole journal. Users who want synchronisation can place the journal directory inside a folder managed by their preferred file synchronisation service. Journaler itself does not depend on a cloud service for operation.
This is free and open source software.
complexipy - fast cognitive complexity analyser for Python
Unlike traditional cyclomatic complexity measurements, which concentrate on the number of independent paths through a program, cognitive complexity attempts to estimate how difficult code is for a human reader to follow. It considers factors such as nested control structures and interruptions to normal program flow.
The application can analyse individual files or entire projects, report functions exceeding configurable complexity thresholds and compare results against earlier Git revisions. It also offers editor integration and can be incorporated into automated code quality checks. This is free and open source software.
zns - fast command-line DNS client
A specific resolver can be supplied when you do not want to use the default DNS server. For scripting, zns offers JSON output together with a short-output mode that prints only record values. Failed queries return a non-zero exit status, allowing shell scripts to respond to errors reliably.
Queries can be performed concurrently, and output can also be written to a file. Taken together, these features make zns suitable for both interactive DNS investigation and automated workflows.
This is free and open source software.