Search Results for "multiple sequence alignment" - Page 3
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Showing 231 open source projects for "multiple sequence alignment"
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CodeGen
Open-source model for program synthesis
CodeGen is a family of open-source large language models designed specifically for program synthesis and code generation tasks. Developed by Salesforce Research, the models are trained on large datasets containing both natural language and programming language content. This allows them to translate natural language descriptions into functional code across a variety of programming languages. CodeGen supports multi-turn program synthesis, meaning it can generate complex programs through a... -
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Qwen2.5-Math
A series of math-specific large language models of our Qwen2 series
Qwen2.5-Math is a series of mathematics-specialized large language models in the Qwen2 family, released by Alibaba’s QwenLM. It includes base models (1.5B / 7B / 72B parameters), instruction-tuned versions, and a reward model (RM) to improve alignment. Unlike its predecessor Qwen2-Math, Qwen2.5-Math supports both Chain-of-Thought (CoT) reasoning and Tool-Integrated Reasoning (TIR) for solving math problems, and works in both Chinese and English. It is optimized for solving mathematical... -
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dLLM
dLLM: Simple Diffusion Language Modeling
...Unlike traditional autoregressive models that generate text sequentially token by token, diffusion language models generate text through an iterative denoising process that refines masked tokens over multiple steps. This approach allows models to reason over the entire sequence simultaneously and potentially produce more coherent outputs with bidirectional context. The project provides an integrated pipeline that standardizes how diffusion language models are trained, evaluated, and deployed, helping researchers reproduce experiments and compare results more easily. ... -
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Learn Claude Code
Bash is all you need, write a claude code with only 16 line code
Learn Claude Code is an educational repository that teaches how modern AI coding agents work by walking learners through a sequence of progressively more complex agent implementations, starting with a minimal Bash-based agent and culminating in agents with explicit planning, subagents, and skills. It emphasizes a hands-on learning path where each version (from v0 to v4) adds conceptual building blocks like the core agent loop, todo planning, task decomposition, and domain knowledge skills,... -
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UglifyJS 3
JavaScript parser, mangler, compressor, beautifier toolkit
UglifyJS is a JavaScript compressor/minifier written in JavaScript. It also contains tools that allow one to automate working with JavaScript code. A parser which produces an abstract syntax tree (AST) from JavaScript code. A code generator which outputs JavaScript code from an AST, also providing the option to get a source map. A compressor (optimizer). it uses the transformer API to optimize an AST into a smaller one. A mangler, reduce names of local variables to (usually) single-letters.... -
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TreeScope
Use dynamic trees to increase interactability with sequence data.
> See TreeScope wiki: https://sourceforge.net/p/treescope/wiki/Home/ Related Software: 1. CStone: https://sourceforge.net/projects/cstone/ 2. CSReadGen: https://sourceforge.net/projects/csreadgen/ 3. CView: https://sourceforge.net/projects/cview/ 4. ChimSim: https://sourceforge.net/projects/chimsim/ 5. TVScript: https://sourceforge.net/projects/tvscript/ 6. SeQuester: https://sourceforge.net/projects/sequester/ 7. TreeScope. (See wiki) -
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Git Interactive Rebase Tool
Native cross-platform full feature terminal-based sequence editor
Native cross-platform full feature terminal-based sequence editor for interactive rebase in Git 1.7.8+. Built and works on Linux, macOS, Windows and many others. Easily set the action to pick, squash, fixup, edit, reword and drop. Reorder the action list with a single key press. Change action and reorder multiple lines at once with visual mode. View the commit overview, and a full commit diff with a press of a key. -
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BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. Please cite the BRIG paper if BRIG is used to generate figures for publications: NF Alikhan, NK Petty, NL Ben Zakour, SA Beatson (2011) BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons, BMC Genomics, 12:402. PMID: 21824423
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OpenSign
🔥 The free & Open Source DocuSign alternative
The premier open source document signing solution (DocuSign alternative). Welcome to OpenSign, the premier open source docusign alternative - document e-signing solution designed to provide a secure, reliable and free alternative to commercial esign platforms like DocuSign, PandaDoc, SignNow, Adobe Sign, Smartwaiver, SignRequest, HelloSign & Zoho sign. Our mission is to democratize the document signing process, making it accessible and straightforward for everyone. -
Build Agents and Models on One PlatformGemini Enterprise Agent Platform is Google Cloud's comprehensive platform for developers to build, scale, govern, and optimize agents and models. Choose from Google's most advanced models and third-party models like Anthropic's Claude Model Family.
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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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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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SheetAtlas
Search and compare data across multiple Excel files instantly
SheetAtlas is a free, cross-platform tool for searching and comparing multiple Excel files as a unified database. 100% offline — your data never leaves your computer. KEY FEATURES Unified Search Load unlimited files (.xlsx, .xls, .csv) and search across all sheets with regex support. Row Comparison Compare rows from different files with intelligent column mapping and visual diff highlighting. Data Export Export to Excel or CSV with column filtering, semantic names, data... -
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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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SoniTranslate
Synchronized Translation for Videos
SoniTranslate is a video translation and dubbing system that produces synchronized target-language audio tracks for existing video content. It provides a web UI built with Gradio, allowing users to upload a video, choose source and target languages, and then run a pipeline that handles transcription, translation and re-synthesis of speech. Under the hood, it uses advanced speech and diarization models to separate speakers, align audio with timecodes and respect subtitle timing, which lets... -
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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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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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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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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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Bert-VITS2
VITS2 backbone with multilingual-bert
...It provides emotional modeling through “emo embeddings,” allowing voices to be conditioned on different affective states during synthesis. Releases include optimizations for Japanese and English alignment, expanded training data, spec caching and pre-generation tools, as well as ONNX export for more lightweight inference deployments. -
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CPAT
RNA coding potential assessment tool
...While still very useful, these approaches have several limitations: Most lncRNAs are less conserved and tend to be lineage specific which greatly limit the discrimination power of alignment-based methods. For example, of 550 lncRNAs detected from zebrafish, only 29 of them had detectable sequence -
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InternLM
Official release of InternLM series
InternLM is an open-source family of multilingual foundation and chat models, accompanied by an ecosystem that supports training, inference, and application development. The repository highlights multiple model sizes intended to serve different needs, from efficient research and prototyping to more capable deployments for complex scenarios. Beyond model weights, the project emphasizes an ecosystem view, pointing developers to compatible tools and projects across training and inference so... -
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LLMDataHub
Quick guide (especially) for trending instruction finetuning dataset
...The repository also highlights datasets suitable for reinforcement learning from human feedback and other alignment strategies used in modern language model training. -
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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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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...
