Search Results for "alignment" - Page 10
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Showing 492 open source projects for "alignment"
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SVPhylA
SVPhylA: Sequence Vectorization for Phylogenetic Analyses
SVPhylA is a python tool for the calculation of several alignment-free distances for phylogenetics analysis from the most popular alignment-free approaches. Such alignment-free methods basically encode DNA and protein sequences (fasta files) into numerical vectors allowing the calculation of alignment-free distances which may be combined into a consensus/compromise matrix by using algorithms like DISTATIS based on Multidimensional Scaling (MSD), Lineal Principal Component Analysis (PCA) and PCA-Kernel (non-lineal). ... -
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Spaced Words Projection (SWeeP), is an application tool capable of generate phylogenetic trees from a large pool of sequences in a reasonably amount of time. It's the method implementation based on an alignment-free technique, capable of represent biological sequences using relatively small vectors while preserving inter-sequence comparability.
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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. ... -
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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.
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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. -
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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. -
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Ruler for windows
Measure, inspect and test tool.
Ruler is a lightweight tool for Windows. It allows you to measure the size and distance between elements on the screen in pixels. -
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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. -
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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. -
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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. ... -
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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 -
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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. -
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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. ... -
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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.
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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. -
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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. -
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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. ... -
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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.
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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. -
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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. ...
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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. -
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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. -
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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.
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Sudamod
SudaMod is a custom Rom made based on Lineage OS
SudaMod is a custom Rom made based on Lineage OS and has given keen priority for the Performance and battery. This Rom is Bundled with many features which you will love to have in any of your Custom Roms. -
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php Kitchen Planner
A complete free web-based 3D interior planning script.
Mainly there are 3 ways of getting php Kitchen Planner to work for your website: (1). The first one is the subdomain installation working as a separate web application along your website. (example: www. yoursite. com, and planner application url will be something like: 3dplanner. yoursite. com) The above option is the most common integration, quick and affordable. For the below options you need to have a eCommerce type of website selling furniture assets: (2). The second way is...