Search Results for "msa"
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Showing 26 open source projects for "msa"
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BrightGauge, a ConnectWise solution, was started in 2011 to fill a missing need in the small-to-medium IT Services industry: a better way to manage data and provide the value of work to clients. BrightGauge Software allows you to display all of your important business metrics in one place through the use of gauges, dashboards, and client reports. Used by more than 1,800 companies worldwide, BrightGauge integrates with popular business solutions on the market, like ConnectWise, Continuum, Webroot, QuickBooks, Datto, IT Glue, Zendesk, Harvest, Smileback, and so many more. Dig deeper into your data by adding, subtracting, multiplying, and dividing one metric against another. BrightGauge automatically computes these formulas for you. Want to show your prospects how quick you are to respond to tickets? Show off your data with embeddable gauges on public sites.
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Our visitor management system streamlines registration, check-in, and authorization processes, while our facility management tools streamline room booking, resource allocation, and asset management. We prioritize security with our advanced risk mitigation measures, including health and safety protocols, emergency messaging, and robust analytics for thorough auditing.
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Haraka
A fast, highly extensible, and event driven SMTP server
Haraka is a highly scalable node.js email server with a modular plugin architecture. Haraka can serve thousands of concurrent connections and deliver thousands of messages per second. Haraka and plugins are written in asynchronous JS and are very fast. Haraka has very good spam protection (see plugins) and works well as a filtering MTA. It also works well as a MSA running on port 587 with auth and dkim_sign plugins enabled. Haraka makes no attempt to be a mail store (like Exchange or Postfix... -
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OpenFold
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction
OpenFold carefully reproduces (almost) all of the features of the original open source inference code (v2.0.1). The sole exception is model ensembling, which fared poorly in DeepMind's own ablation testing and is being phased out in future DeepMind experiments. It is omitted here for the sake of reducing clutter. In cases where the Nature paper differs from the source, we always defer to the latter. OpenFold is trainable in full precision, half precision, or bfloat16 with or without... -
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Alphafold2
Unofficial Pytorch implementation / replication of Alphafold2
To eventually become an unofficial working Pytorch implementation of Alphafold2, the breathtaking attention network that solved CASP14. Will be gradually implemented as more details of the architecture is released. Once this is replicated, I intend to fold all available amino acid sequences out there in-silico and release it as an academic torrent, to further science. Deepmind has open sourced the official code in Jax, along with the weights! This repository will now be geared towards a... -
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NekoHyperSeed
NekoHyper Seed Modified Xiaomi HyperOS for marble/marblein device
Feature: no binary modification (except TWRP and melt kernel) and only added minimal config file modification needed by feature unlock to keep every thing user-side trusted and reviewable Stable and keep updated to Xiaomi offical You can keep your userdata after each update Unlock features without losing security -
Yooz provides the smartest, most powerful, and easiest-to-use cloud-based E-invoicing and Purchase-to-Pay automation solution. It delivers unmatched savings, speed, and security with affordable zero-risk subscriptions to more than 5,000 customers and 300,000 users worldwide.
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UniSIMD-assembler
SIMD macro assembler unified for ARM, MIPS, PPC and x86
.../SSE4 and AVX/AVX2/AVX-512 (32/64-bit x86 ISAs), ARMv7 NEON/NEONv2, ARMv8 AArch32 and AArch64 NEON, SVE (32/64-bit ARM ISAs), MIPS 32/64-bit r5/r6 MSA and POWER 32/64-bit VMX/VSX (little/big-endian ISAs) are mostly implemented (/w horizontal reductions) although scalar improvements, wider SIMD vectors with zeroing/merging predicates in 3/4-operand instructions are planned as extensions to current 2/3-operand SPMD-driven vertical SIMD ISA. See README file. -
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QuadRay-engine
Realtime raytracer using SIMD on ARM, MIPS, PPC and x86
.../SSE4 and AVX/AVX2/AVX-512 (32/64-bit x86 ISAs), ARMv7 NEON/NEONv2, ARMv8 AArch32 and AArch64 NEON, SVE (32/64-bit ARM ISAs), MIPS 32/64-bit r5/r6 MSA and POWER 32/64-bit VMX/VSX (little/big-endian ISAs) are mostly implemented (/w horizontal reductions) although scalar improvements, wider SIMD vectors with zeroing/merging predicates in 3/4-operand instructions are planned as extensions to current 2/3-operand SPMD-driven vertical SIMD ISA. See README file. -
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A script to take orthomcl cluster output and fasta file with all clustered sequences, to generate a MSA per cluster, folllowed by alignment trimming and tree generation.
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The Bahasa wordnet is a semantic network for the Malay languages, currently covering both Malaysian and Indonesian. It uses the structure of WordNet and is open source.
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SysAid is an ITSM, Service Desk and Help Desk software solution that integrates all of the essential IT tools into one product. Its rich set of features include a powerful Help Desk, IT Asset Management, and other easy-to-use tools for analyzing and optimizing IT performance.
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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...
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PADIC
A multilingual Parallel Arabic DIalectal Corpus
PADIC (Parallel Arabic DIalectal Corpus) is a multi-dialectal corpus built in the framework of the National Research Project "TORJMAN", led by Scientific and Technical Research Center for the Development of Arabic Language and funded by the Algerian Ministry of Higher Education and Scientific Research. PADIC is composed of 6 dialects: two Algerian dialects (Algiers and Annaba cities), Palestinian, Syrian, Tunisian, Moroccan) and MSA. Mourad Abbas Computational Linguistics Department... -
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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... -
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Multiple Sequence Alignment using DP
Dynamic Programming (DP) is widely used in Multiple Sequence Alignment
Multiple sequence alignment (MSA) is an important problem in molecular biology. Biological sequences are aligned with each other vertically to show possible similarities or differences among these sequences. The similarities may reveal evolutionary history and are clues about common biological functions of the sequences. The information of similarity and difference can then be used to predict the secondary or tertiary structure of new sequences and to find the relationships between... -
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REDHORSE
Software suite for the analysis of haploid hybrids using NGS
The alignments to the genome from next-generation-sequencing (NGS) data cannot be directly used as input to the existing recombination detection (RD) algorithms that use multiple sequence alignments (MSA). We therefore designed a software suite called REDHORSE that takes genomic alignments as input, extracts meaningful markers and generates MSAs that are the inputs to existing RD algorithms. In addition, REDHORSE implements a custom RD algorithm that makes use of sequence information... -
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AlignMerger
A tool for merging two large multiple sequence alignments
AlignMerger is useful to merge two sets of multiple sequence alignments (MSA). It can greatly reduce the computational time needed to construct a MSA, compare to others commonly used MSA tools. Inputs required for the tool are two MSAs in FASTA format and output of the tool is a merged MSA in FASTA format. -
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CEMAsuite
Consensus/Degenerate Primer Design Application
CEMAsuite, is an interactive Java-based application with the ability to (i) construct a codon-equivalent multiple alignment (CEMA) from a protein multiple sequence alignment (MSA) file, (ii) generate and score each position in the consensus DNA sequence using multiple algorithms, (iii) design single-degeneracy primer backbones using Primer3 (Untergasser et al. 2012), (iv) estimate the stability of degenerate primers on each of the coding sequences within the CEMA, and (v) export intermediate... -
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EDNA
Energy Based Multiple Sequence Alignment (MSA) for Binding Sites
Multiple Sequence Alignment for Transcription Factor Binding Sites using Di nucleotides dependencies and relying on Free Interaction energies between neighbouring DNA bases to stabilise substitution energy of the alignment. http://www.ncbi.nlm.nih.gov/pubmed/23990411 -
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MSA-CUDA: multiple sequence aligner
multiple sequence alignment on CUDA-enabled GPUs.
This project is not active any more since we failed to get the permit from the Clustal team to distribute our software. You can refer to the paper "Yongchao Liu, Bertil Schmidt, Douglas L Maskell:MSA-CUDA: multiple sequence alignment on graphics processing units with CUDA. ASAP 2009" for more details. -
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GenNon-h
Simulating non-homogeneous multiple sequence alignments
A number of software packages are available to generate DNA MSAs evolved under continuous-time Markov processes on phylogenetic trees. On the other hand, methods of simulating the DNA MSA directly from the transition matrices do not exist. Moreover, existing software restricts to the time-reversible models and it is not optimized to generate nonhomogeneous data (i.e. placing distinct substitution rates at different lineages). GenNon-H is the first package designed to generate multiple... -
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MSA noise reduction
sequence noise reduction
A simple method to reduce the noise in multiple sequence alignment -
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MSA2SNP is a tool for mining SNP sites in multiple sequence alignment (MSA). This tool inherits the easy-to-use interface from MEGA4 Explorer with advance data presentation. MSA2SNP lets you visualize alignments and import from CLUSTAL program directly.
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