Search Results for "multiple sequence alignment" - Page 5
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Showing 231 open source projects for "multiple sequence alignment"
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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. -
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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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M80AttributedLabel
Another attributed label using CoreText
M80AttributedLabel is a feature-rich UILabel alternative that supports rich text rendering with advanced formatting options. It allows embedding links, images, and custom text styling within a label, supporting complex layouts. -
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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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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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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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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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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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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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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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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. ... -
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SUPERmerge
ChIP-seq coverage island analysis algorithm for broad histone marks
...SUPERmerge is especially useful for investigating low sample size ChIP-seq experiments in which epigenetic histone modifications (e.g., H3K9me1, H3K27me3) result in inherently broad peaks with a diffuse range of signal enrichment spanning multiple consecutive genomic loci and annotated features. -
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Buckets
A complete, fully tested and documented data structure library
...Dictionaries map keys to values, each key can map to at most one value. A heap is a binary tree that maintains the heap property. Every node is less than or equal to each of its children. A linked list is a sequence of items arranged one after another. A multi dictionary is a special kind of dictionary that holds multiple values against each key. In a priority queue, each element is associated with a "priority", and elements are dequeued in the highest-priority-first order (the elements with the highest priority are dequeued first). -
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MSTgold
Estimate minimum spanning trees with statistical bootstrap support
...The MSTgold package includes Mac OS X, Linux, and Windows executables of the MSTgold program, a detailed Manual, example data and results, and executables of the program Fasta2MSTG which converts Fasta sequence files to the MSTgold input format. -
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SW#
smith waterman, gpu, cuda, alignment
SW# (swsharp) is a library for sequence alignment based on CUDA enabled GPUs. It utilizes Hirschbergs and Ukkonens algorithm for memory efficiency and additional speed up. The library is scalable for use with multiple GPUs. Some parts of the library utilize MPI for CUDA enabled clusters. This work has been supported in part by Croatian Science Foundation under the project UIP-11-2013-7353. -
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PPA D
A method for predicting the locations of protein antigenic determinant
...A means of locating multiple antigenic sites on a homologous series of proteins -
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RED
RED-RNA Editing sites Detector.
RED(RNA Editing Detector) is a program to detect and visualise RNA editing events at genomic scale using next-generation sequencing data. RED can also be used in command line. RNA editing is one of the post- or co-transcriptional processes with modification of RNA nucleotides from their genome-encoded sequence. In human, RNA editing event occurs mostly by deamination of adenosine to inosine (A-to-I) conversion through ADAR enzymes.
