Search Results for "alignment" - Page 10
Sort By:
Showing 522 open source projects for "alignment"
View related business solutions-
Ship Agents FasterGemini Enterprise Agent Platform lets you rapidly build, scale, govern and optimize production-ready agents grounded in your organization's data. The platform enables developers to build custom or pre-built agents for virtually any use case. New customers get $300 in free credits.
-
Go from Code to Production URL in SecondsSkip the Kubernetes configs. Cloud Run handles HTTPS, scaling, and infrastructure automatically. Two million requests free per month.
-
1
seqdiva
SeqDivA:Sequence Diversity Analysis
Sequence Diversity Analysis - SeqDivA version 1.0 is a python-based tool with a friendly GUI designed for Linux and Mac OS. Utility: Run alignment algorithms (water, needle, and blast) to compare all-vs.-all protein, DNA, and RNA sequences. SeqDivA provides similarity, identity, and bit-score matrixes and dot plots to explore/illustrate the diversity (homology degree) of the sequences, enabling the delimitation of the twilight zone. Installation: - Download SeqDivA - decompress the “.zip or tar.gz” file - Load the graphical interface by executing python SeqDivA.py. ... -
2
LMAP_S
Lightweight Multigene Alignment and Phylogeny eStimation
Emanuel Maldonado and Agostinho Antunes (2019) LMAP_S: Lightweight Multigene Alignment and Phylogeny eStimation. BMC Bioinformatics, 20:739. doi: https://doi.org/10.1186/s12859-019-3292-5 -
3
TI2BioP allows mainly the calculation of topological indices (spectral moments) derived from inferred and artificial 2D structures of DNA, RNA and proteins being possible to carry out a structure-function correlation irrespective of sequence alignments. TI2BioP version 3.0 is a python platform with a graphical interface designed for Windows, Linux and Mac OS.
-
4
monolingual-sentence-aligner
Monolingual Sentence Aligner
- algorithm.js class Alignment: represents a sentence alignment, in the form of bigraph. - data.js class Sentences: represents a list of sentences. Its constructor receives a string and splits them into sentences. class Diff: represents a diff file. Its constructor processes a diff string and splits them into tokens, including sentence boundaries. -
Demo Series - Small Business Backup By VeeamWatch this on-demand demo series and learn how to protect your Microsoft 365 data with clear, simple, actionable steps that are easy to implement for businesses of all sizes.
-
5
RGT
Repeat Genotyping Tool
Alignment-free genotyping software for simple sequence repeat structures from targeted sequencing reads Simple sequence repeat structures are often genotyped using targeted sequencing, where thousands of sequence reads from the same locus are generated. These reads are then aligned to thousands of reference sequences representing all possible repeat structures that might exist in the sample. -
6
CMU Sphinx
Speech Recognition Toolkit
Thank you for visiting! ----> Maintenance and improvement work has MOVED to https://cmusphinx.github.io/ Please go there for the most recent software and documentation. <---- CMUSphinx is a speaker-independent large vocabulary continuous speech recognizer released under BSD style license. It is also a collection of open source tools and resources that allows researchers and developers to build speech recognition systems. -
7
UnsupervisedMT
Phrase-Based & Neural Unsupervised Machine Translation
...Training relies on denoising auto-encoding and back-translation, with on-the-fly, multithreaded generation of synthetic parallel data to continually refresh supervision signals. The project also provides scripts to fetch and preprocess monolingual data, learn BPE codes, and train cross-lingual embeddings that bootstrap unsupervised alignment between languages. Beyond the core EMNLP 2018 setup, the codebase exposes additional, optional capabilities such as multi-language training, language model pretraining with shared parameters, and adversarial training. -
8
PTESFinder
Post-Transcriptional Exon Shuffling (PTES) Identification Pipeline
...PTESFinder leverages the power of established RNASeq tools and systematically excludes all known classes of false positive structures by applying stringent filters designed to specifically target these false positives. PTESFinder compares alignment qualities of reads mapping to putative PTES structures with qualities of the same reads when mapped to genomic regions and canonically spliced transcripts. This approach increases the confidence in PTES supporting reads. Reads emanating from template-switching events are often characterised by large indels when aligned to the transcriptome. ... -
9
MUSE
A library for Multilingual Unsupervised or Supervised word Embeddings
MUSE is a framework for learning multilingual word embeddings that live in a shared space, enabling bilingual lexicon induction, cross-lingual retrieval, and zero-shot transfer. It supports both supervised alignment with seed dictionaries and unsupervised alignment that starts without parallel data by using adversarial initialization followed by Procrustes refinement. The code can align pre-trained monolingual embeddings (such as fastText) across dozens of languages and provides standardized evaluation scripts and dictionaries. By mapping languages into a common vector space, MUSE makes it straightforward to build cross-lingual applications where resources are scarce for some languages. ... -
Custom VMs From 1 to 96 vCPUs With 99.95% UptimeLive migration and automatic failover keep workloads online through maintenance. One free e2-micro VM every month.
-
10
Batch PIE
A batch pipelined image editor
Current filter functionality: - Simple editing options: Image cropping, resizing, rotation, Color brightness curve alignment - Histobram processing: Convolution, statistics (e. g. f_max or median analysis) - Image segmentation: The actual segmentation process as well as group weight calculation for further filtering (both functions rely on self defined custom dynamic mathematical functions) - Dynamic mathematical functions for custom and automated image filtering: General mathematical operations, using image or matrix as f(x, y), export f(x, y) as image or matrix, mapping variables on other ones and of course boolean operation for case sensitivity - A flexible variables model of dynamic mathematical function that sets no restriction on particular variables count - Sub project support for an organized total process targeting to save time using previously created editing routines instead of redoing steps each time -
11
Offensive Web Testing Framework
Offensive Web Testing Framework (OWTF), is a framework
OWASP OWTF is a project focused on penetration testing efficiency and alignment of security tests to security standards like the OWASP Testing Guide (v3 and v4), the OWASP Top 10, PTES and NIST so that pentesters will have more time to see the big picture and think out of the box. More efficiently find, verify and combine vulnerabilities. Have time to investigate complex vulnerabilities like business logic/architectural flaws or virtual hosting sessions. -
12
Weinberg-CMfinder
Predict and score RNA secondary structures
The CMfinder package is a suite of programs with two main purposes: (1) the cmfinder program infers an alignment and consensus secondary structure of an RNA, using unaligned sequences as input. (2) other tools score alignments to indicate evidence of RNA secondary structure within the alignment. RNAphylo assigns a probabilistic score to an existing alignment, using an explicit phylogenetic model. hmmpair assigns a score based on evidence of covariation that is supported by sequence conservation. ... -
13
The SPInDel workbench is a computational platform to facilitate the planning and management of SPInDel projects, alignment of nucleotide sequences, visualization and selection of conserved regions, calculation of PCR primers properties, prediction of SPInDel profiles and diverse statistical and phylogenetic analyses. It includes a large dataset comprising nearly 1,800 numeric profiles for the identification of eukaryotic, prokaryotic and viral species.
-
14
MyNotes
Sticky notes/post-it application for linux
...They can be organized in categories and each category has a color. Images, checkboxes and a few predefined symbols can be inserted in the notes. The style of the text can be changed (alignment, style, color). -
15
Tacotron-2
DeepMind's Tacotron-2 Tensorflow implementation
...It includes directory layouts and logging directories for multiple datasets such as LJSpeech and M-AILABS en_US/en_UK, making it easier to adapt to new English corpora. Separate log trees track mel-spectrograms, attention plots, evaluation audio, and vocoder outputs, so you can inspect how alignment and audio quality evolve over time. -
16
TaBS-Pipe
Targeted Bisulfite Sequencing Data Analysis Pipeline v1.0.2
...TaBSAP is a pipeline to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step and enables a researcher to analyze the methylation levels of their samples straight away. It's main features are: -Bisulfite mapping and methylation calling in one single step -Supports single-end read alignments -Alignment seed length, number of mismatches etc. are adjustable -The output gives heatmap with categories. -
17
comer
Protein remote homology search tool
COMER is a protein sequence alignment tool designed for protein remote homology detection. It accepts a multiple sequence alignment as input and converts it into the profile to search a profile database for statistically significant similarities. COMER is licensed under the GNU GP License, version 3. Please find its archive file, download and extract it with the command "tar -zxf <archive-name>", and refer to the README file for instructions on how to use the software. ... -
18
Java Text Table Formatter is a Java library that renders tables made of characters. The user add cells and can add format characteristics like predefined/custom table styles, text alignment, abbreviation, column width, border types, colspan, etc.
-
19
face-recognition.js
Simple Node.js package for robust face detection and face recognition
...Developers can compare unknown faces with stored examples and receive ranked predictions with distance values. The package also includes five-point and 68-point facial landmark predictors for alignment and analysis. Synchronous and Promise-based asynchronous methods support different application designs, while OpenCV integration enables additional image processing. OpenBLAS can improve CPU performance when the native dependency is compiled with it. The project is now considered obsolete by its author, who recommends face-api.js for equivalent browser and Node.js functionality. -
20
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. -
21
inGAP-family provides an efficient and effective framework to discover, filter and visualize DNA polymorphisms and structural variants from alignment of short reads. Applying this method on polymorphism detection on real datasets shows that elimination of artificial variants greatly facilitates the precise identification of meiotic recombination points, recognizing causal mutations in mutant genomes or QTL loci. In addition, inGAP-family provides user-friendly graphical interface for detection of polymorphisms and structural variants, and for further evaluation of predicted variants and identification of mutations related to genotypes. ...
-
22
PyTom
http://www.sciencedirect.com/science/article/pii/S1047847711003492
PyTom is a toolbox developed for interpreting cryo electron tomography data. All steps from reconstruction, localization, alignment and classification are covered with standard and improved methods. Please sign up to our mailing list to keep up with the most recent updates and versions. -
23
CoVaMa
Co-Variation Mapper
CoVaMa (Co-Variation Mapper) (python) detects correlated patterns of mutations in a viral quasi-species. CoVaMa takes NGS alignment data (SAM) and populates large matrices of contingency tables that correspond to every possible pairwise interaction of nucleotides or amino acids in the viral genome. These tables are then analysed for evidence linkage disequilibrium. CoVaMa requires python version 2.7 and Numpy. -
24
spark-msna
Algorithm on Spark for aligning multiple similar DNA/RNA sequences
The algorithm uses suffix tree for identifying common substrings and uses a modified Needleman-Wunsch algorithm for pairwise alignments. In order to improve the efficiency of pairwise alignments, an unsupervised learning based on clustering technique is used to create a knowledge base to guide them. -
25
2D Statistical Models. Building: shape model, texture model and concatenated appearance model; Fitting: 1D profile ASM, 2D profile ASM, direct local texture constrained(LTC) ASM, basic AAM, ICIA AAM, IAIA AAM, etc.
