Search Results for "multiple sequence alignment" - Page 4
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Showing 231 open source projects for "multiple sequence alignment"
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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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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).... -
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misc genomics tools
Various scripts used in sequencing, annotation and RNAseq analysis
This is a collection of various programs developed in the course of a genomics project, involving the Pseudomonas strain NCIMB10586 These include * identifying and correcting errors in an (eg) pacbio genome sequence using illumina reads * prokaryotic sequence/genome annotation * RNAseq analysis - normalisation and collation of multiple samples as a group * RNAseq visualisation All scripts are provided on a 'best efforts' basis, however due to various system changes I do not guarantee that all files are the version used in the analysis. ... -
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CLIP Guided Diffusion
A CLI tool/python module for generating images from text
A CLI tool/python module for generating images from text using guided diffusion and CLIP from OpenAI. Text to image generation (multiple prompts with weights). Non-square Generations (experimental) Generate portrait or landscape images by specifying a number to offset the width and/or height. Uses fewer timesteps over the same diffusion schedule. Sacrifices accuracy/alignment for quicker runtime. options: - 25, 50, 150, 250, 500, 1000, ddim25,ddim50,ddim150, ddim250,ddim500,ddim1000 (default: 1000) Prepending a number with ddim will use the ddim scheduler. e.g. ddim25 will use the 25 timstep ddim scheduler. ... -
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XLM (Cross-lingual Language Model)
PyTorch original implementation of Cross-lingual Language Model
...Pretrained checkpoints cover dozens of languages and multiple model sizes, balancing quality and compute needs. -
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m6811dis
M6811 Code-Seeking Disassembler
The M6811 Code-Seeking Disassembler is a command-line tool that lets you enter known starting vectors for a given code image for the 6811 micro. It will disassemble the code and follow through branches to assist in the separation of code and data. Its companion Fuzzy Function Analyzer uses DNA Sequence Alignment Algorithms to locate similar code in multiple binaries, facilitating reverse-engineering. Originally written to analyze code from GM automotive engine controllers, but is useful anywhere a 6811 micro is being used. Version 1.0 was written in Borland Pascal in April 1996, and updated to v1.2 in June 1999. It was later rewritten to C++ in July 1999 through Jan 2000. ... -
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Nexplorer is a web-based phylogenetic browser, used to view and edit comparative data, and ideal for creating publication-quality views in which the tips of a tree are aligned with the rows of a character matrix (e.g., a sequence alignment).
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ATSCAN SCANNER
Advanced dork Search & Mass Exploit Scanner
Advanced Mass Search / Dork / Exploitation Scanner. -
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x-spreadsheet
A web-based JavaScript (canvas) spreadsheet
...These parameters are loaded in the first instantiation, and can also be set later, but it is recommended to modify and load in advance the changes that you need to change. You can adjust the number of columns displayed by default len, AZ, the default width of each column, the default width widthof the left sequence column indexWidth, and the default minimum width of each columnminWidth. You can adjust the style of table rendering. Some of the features include undo and redo, paint format, clear format, format, font, font size, font bold, font italic,, underline, strike, text color, fill color, borders, merge cells, align, text wrapping, freeze cell, functions, resize row-height, col-width, copy, cut, paste, autofill, insert row, column, delete row, column, hide row, column, multiple sheets, print, and data validations. -
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SwiftUI Drawer
A SwiftUI bottom-up controller, like in the Maps app
...It also provides customization options such as alignment, width, and responsive layout adjustments depending on device orientation or screen size. -
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TFKit
Handling multiple nlp task in one pipeline
TFKit is a tool kit mainly for language generation. It leverages the use of transformers on many tasks with different models in this all-in-one framework. All you need is a little change of config. You can use tfkit for model training and evaluation with tfkit-train and tfkit-eval. The key to combine different task together is to make different task with same data format. All data will be in csv format - tfkit will use csv for all task, normally it will have two columns, first columns is the... -
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A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.
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A Java library for evolutionary biology and bioinformatics, including objects representing biomolecular sequences, multiple sequence alignments and phylogenetic trees.
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Jack LIRE (Linked Record)
Quantum universal object system with referencing and genetics
Jack LIRE (Linked Record) is a quantum database-backed life-long text record diary with referencing (linking) between records, and a data library for life-long keeping of files such as documents, photographs, music and more. The diary records are fully searchable. Files can be mentioned in diary records to preserve memories, document knowledge and ideas, and more. Massive numbers of diary records and files can be permanently kept. A database located on one computer can be accessed from... -
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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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An alignment-free standalone tool with interactive graphical user interface for DNA sequence comparison and analysis
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QtShowRunner
Runs a looping sequence of LibreOffice Impress Slide Shows
QtShowRunner is a program to chain together multiple LibreOffice impress slide shows. Each show in the sequence is set under Slide Settings so that mouse clicks do not advance the slides. This is important. QtShowRunner launches each show in the sequence and then clicks the mouse every few seconds and when the last black screen is shown, the mouse click terminates the show and Impress exits. -
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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... -
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Mousetrap
Simple library for handling keyboard shortcuts in Javascript
...Mousetrap has been tested and should work in Internet Explorer 6+, Safari, Firefox, and Chrome. The bind method is the main call you will be making. This will bind a specified keyboard command to a callback method. If you want to bind multiple key commands to the same callback you can pass in an array for the first argument. Mousetrap 1.4 introduced a generic mod helper which lets you set cross platform shortcuts. The sequence of keys feature was inspired by Gmail. Any keys separated by a space will be considered a sequence. If you type each key in order the final one in the sequence will trigger the callback. ...
