Search Results for "multiple sequence alignment" - Page 5
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Showing 311 open source projects for "multiple sequence alignment"
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Satsuma
Whole-genome synteny alignments
...Parallelization is built-in. Grabherr, M. G., Russell, P., Meyer, M., Mauceli, E., Alföldi, J., Di Palma, F., & Lindblad-Toh, K. (2010). Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics, 26(9), 1145-51. For more information, documentation and recent activity, please check out our project web page: http://satsuma.sourceforge.net/ -
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C++ Math Expression Parser
C++ Math Expression Parser Library
The C++ Mathematical Expression Toolkit Library (ExprTk) is a simple to use, easy to integrate and extremely efficient run-time mathematical expression parser and evaluation engine. ExprTk supports numerous forms of functional, logical and vector processing semantics and is very easily extendible. Download http://partow.net/programming/exprtk/index.html -
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Serial Tool
Serial Tool for developing serial communication with embedded systems.
PROJECT MOVED TO: https://github.com/damogranlabs/serial-tool See releases page: https://github.com/damogranlabs/serial-tool/releases Serial Tool is a utility for developing serial communications, custom protocols or device testing. You can set up bytes to send accordingly to your protocol and save configuration to a file – which can be used another time. You can send multiple byte arrays, you can send sequence of different byte arrays and put delay between them. You can read data in HEX or ASCII. You can even write a note to yourself like: “CH1: toggle LED 1”. -
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UnsupervisedMT
Phrase-Based & Neural Unsupervised Machine Translation
Unsupervised Machine Translation is a research repository that implements both phrase-based SMT and neural MT approaches for translation without parallel corpora. The neural component supports multiple architectures—seq2seq, biLSTM with attention, and Transformer—and allows extensive parameter sharing across languages to improve data efficiency. 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. ... -
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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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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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Tacotron-2
DeepMind's Tacotron-2 Tensorflow implementation
...The repository is structured as a full training pipeline: dataset preparation, preprocessing into spectrograms, Tacotron training, WaveNet (or Griffin-Lim) vocoder training, and final waveform synthesis. 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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GMOL
A tool for 3D genome structure visualization
GMOL is an application designed to visualize genome structure in 3D. It allows users to view the genome structure at multiple scales, including: global, chromosome, loci, fiber, nucleosome, and nucleotide. This software was built upon the pre-existing Jmol package by Prof. Cheng's group. The software is developed in Prof. Jianlin Cheng's Bioinformatics, Data Mining and Machine Learning Laboratory in the Computer Science Department at the University of Missouri - Columbia, USA. The project... -
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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. -
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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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Keypress
A keyboard input capturing utility
Keypress is a JavaScript utility (Apache‑2.0) for defining keyboard combos, sequences, and custom modifiers. Popular in game development and interactive web apps, it supports keydown/keyup, multiple modifiers, sequence combinations, and offers ~9 KB footprint with zero dependencies. -
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idwtree
Assigns orthologs using a phylogenetic tree
...Build a multiple sequence alignment of BLAST hits with reference sequences (e.g. with CLUSTAL OMEGA or MAFFT). 4. Use the alignment to build a phylogenetic tree (e.g. with the PHYLIP package) 5. Use idwtree to assign BLAST hits to ortholog groups -
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FreeFileSync
Free data backup software to synchronize files and folders
FreeFileSync is a free Open Source software that helps you synchronize files and synchronize folders for Windows, Linux and macOS. It is designed to save your time setting up and running data backups while having nice visual feedback along the way. _______________________________________________________________ DOWNLOAD LINKS (official homepage): https://freefilesync.org/ -
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PROPAB
PROPensity for Alpha and Beta
PROPAB: Computation of Propensities and Other Properties from Segments of 3D structure of Proteins Authors: Rifat Nawaz UL Islam1, Chittran Roy2, Parth Sarthi Sen Gupta3, Debanjan Mitra2, Sahini Banerjee4 and Amal Kumar Bandyopadhyay2* 1Department of Zoology, The University of Burdwan, West Bengal, 713104, India 2Department of Biotechnology, The University of Burdwan, West Bengal, 713104, India 3Department of Chemistry, IISER, Berhampur, Odisha, 760010, India 4Department of... -
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MetaModelManager
MetaModel Manager for transdisciplinary species risk assessment
Metamodels provide a novel approach to species risk assessment in which diverse threats are addressed through different disciplines, act at different spatiotemporal scales, or interact in non-linear ways. A metamodel links multiple, discrete models that depict components of a complex system, governing the flow of information between models and the sequence of events in the simulation. Each discrete model simulates processes specific to its disciplinary realm while being informed of changes in other parts of the metamodel by accessing common descriptors of the system, populations, and individuals. ... -
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Digit Span Tester
A Task / Test of Working Memory for Cognitive / Neurosciece Research
To perform automated digit span tests to evaluate on working memory function, especially in cognitive / neuro research. Hope to reduce practice effects and eliminate the need to use clinical assessments in research settings. Requires Java 7 or newer. Note that this is a research tool, and was not intended (and not evaluated) for clinical assessment. FINAL VERSION: If you want more features, download the source and hack it yourself. Apologies to those who've asked for help and got no... -
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Genome Profiler
a wgMLST analysis tool for bacterial WGS data
Genome Profiler (GeP) is a program to perform whole-genome multilocus sequence typing (wgMLST) analysis for bacterial isolates. Please note that this program is designed to run in Unix-like operating systems such as Mac OS X or Linux. GeP uses conserved gene neighborhoods (CGN) to resolve gene paralogy. This approach allows the differentiation of orthologs from recently duplicated paralogs, which are often indistinguishable by pairwise sequence alignment. ... -
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IPAS is a new and practial iterative progressive multiple sequence alignment algorithm, used to align protein sequences, which is a close variant of the MUSCEL algorithm. However, based on the gene sequences length, our algorithm starts either with the "kmer" distance table or with the "Dynamic Programming (DP)" distance table. The other steps of this algorithm include: generating a Guide-tree using UPGMA, multiple sequence alignments, "kimura" distance calculation from aligned sequences and new techniques to improve multiple sequence alignments. ...
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IPAS for protein sequences
multiple alignment algorithm for protein sequences
IPAS is a new and practial protein multiple sequence alignment algorithm based on iterative progresive alignment algorithm Assessed on BAliBASE 3.0, PREFAB 4.0, SABMARK 1.65, and OXBENCH, MSAProbs achieves the statistically highest alignment accuracy, compared to ClustalW 2.0.10, MAFFT 6.717( using L-INS-i with --maxiterate = 1000), MUSCLE 3.8.31, ProbCons 1.12, and Probalign 1.3. -
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Highlight Library
A library for app directivity highlighting
Highlight is an Android onboarding and guidance library that draws an overlay to visually emphasize specific UI elements and attach tip content, helping users discover features inside an app. It works by placing a translucent mask over a chosen “anchor” area (often the activity content view) and then “cutting out” or spotlighting target views so they stand out clearly. Developers can define one or more highlighted targets, supply a custom tip layout (for example, an arrow plus text), and... -
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SimpleTAG
Massive audio tagger
SimpleTag is a cross-platform desktop tool, which allows to update the labels of all your music before incorporating it into a musical library or cloud service. Nowadays, the amount of music we have in our equipment is so large, it is no longer possible to manage with the traditional system of filenames and directories. The most convenient is to use the concept of libraries that handle the big market music players: iTunes, Amarok, Windows Media Player, Google Music, ..etc The labels... -
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High Speed Parallel Imaging (HSPI)
HSPI does parallel capture and sky surveys.
HSPI offers to the astronomer the possibility to capture pictures from the CCD camera in a fast and intuitive way, keeping under control all the instrumentation in posses. HSPI can control the CCD camera, the mount, the focuser, the filter wheel and the dome from a single interface, and not only this: these features can be added on as many observatories and instrumentations you want. HSPI is ASCOM and INDI compatible, so if you want to use particular setups like Linux computers connected... -
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A tool for finding missing or corrupt images in a sequence. Also generates basic statistics from Exif data. Targeting time-lapse and render-farm users when using post-processing tools such as After Effects.
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AKtoolbox
Matlab Toolbox for coevolution analysis of multiple sequence alignment
AK Toolbox is a Matlab Toolbox for co-evolution analysis for protein Multiple Sequence Alignment (MSA) distributed under Simplified BSD License. The aim of AK toolbox is to provide a set of Matlab functions, which are independent of Matlab Bioinforamtics Toolbox, for coevolution anaylsis for MSA. At present, co-evolution methods available in this package are Statistical Coupling Analysis (SCA), Explicit Likelihood of Subset Covariance (ELSC), Mutual Information (MI), Observed Minus Expected Square method (OMES), McLanhlan Based Substitution Correlation (MCBASC), Direct-coupling analysis (DCA) and logR. ...
