Search Results for "align" - Page 5
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Showing 152 open source projects for "align"
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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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Flex Layout Attribute (FLA)
HTML layout helper based on CSS flexbox specification
...FLA is defined with two custom HTML attributes. Layout, use it on the container (parent) element to set layout of its children elements. And self, use it on container/child element to set size or align for the element itself. -
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FXPad
A lightweight, easy-to-use portable notepad.
FXPad is a lightweight, easy-to-use portable notepad. With good optimalization, and it's small disk usage, it's one of the best notepads right now. -
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vim-easy-align
A Vim alignment plugin
vim-easy-align is a Vim/Neovim plugin that makes it simple to align text by a pattern, character, or regular expression across a selection or motion. Instead of hand-inserting spaces and fiddling with tabs, you select lines and invoke an interactive prompt that previews the alignment as you type the rule. It supports multiple delimiters—commas, colons, equals signs, pipes—and can align on the nth occurrence or on complex regex groups. -
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LAMSA
Long Approximate Matches-based Split Aligner
LAMSA (Long Approximate Matches-based Split Aligner) is a novel split alignment approach with faster speed and good ability of handling SV events. It is well-suited to align long reads (over thousands of base-pairs). -
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function qualityGuide
A JavaScript Quality Guide
...It provides concrete examples of good and bad practices for strings, variable declarations, conditionals, prototypes, object and array literals, regular expressions, and console usage. There are also recommended .editorconfig and .jshintrc templates, giving teams a ready-made configuration to align editors and linters. The document is meant to be forked, adapted, and shared internally so that teams can converge on a “sweet spot” that encourages quality without becoming dogmatic. -
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Afterglow Theme
A minimal dark Theme for Sublime Text 2 and 3
...The theme adjusts editor chrome—tabs, sidebars, status bars, and panels—so they visually recede and put focus on the buffer. Multiple accent variants and sidebar icon options let you align the look with your project or OS styling. Installation is straightforward through popular package managers, and the settings are simple to tweak for font weight, caret style, and selection emphasis. By balancing saturation and contrast, Afterglow reduces eye fatigue during long sessions while preserving quick visual parsing of complex files. -
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LinxBooks – Have faith and carry on. Overview LinxBook is a simple and easy-to-use business accounting application. Linxbooks includes basic features that help the businesses create invoices, quotations, manage payments, payrolls, contracts and expenses Download at GitHub: https://github.com/LinxHQ/linxbooks Demo is at: http://linxbooks.com/demo (user: admin, password: admin123)
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Spock Example
Spock example specifications along with ready-to-go Gradle builds
...It includes sample Specification classes that illustrate key Spock features—given/when/then style, data-driven testing, mocking/stubbing, and interaction verification. The examples show how to integrate Spock into typical Java/Groovy projects, how to run tests inside IDEs like Eclipse or IntelliJ, and how to align build scripts with Spock’s dependencies. It serves as a learning aid for developers new to Spock or wanting to adopt its expressive syntax in real-world projects. Because Spock has a lot of syntactic expressiveness and unique features (e.g. built-in data tables, concise mocking), seeing concrete samples is especially helpful. The project lowers the barrier to entry by giving readers a working, runnable baseline to experiment with. -
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iAstroHub
Automated astrophotography using mobile devices
iAstroHub is: - the world's first solution for mobile astrophotography. A user can interact with all astrophotography devices from any mobile device using a web browser. - developed by Anat Ruangrassamee, Ph.D., Bangkok Thailand. (aruangra at yahoo dot com) See how it works from here: http://www.youtube.com/watch?v=Sncd3j8ipBQ Requirements and supported devices. 1. Autoguider: Orion Starshoot autoguider, QHY5, QHY5-II, QHY5L-II, QHY6 2. DSLR 3. CCD: QHY5,6,8,8L,9,11,12 4.... -
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Java Wizard Development Framework
Reduced SWING coding. New UI components. Easy layout management.
About: 1) Projects helps Java - SWING developers to develop UI forms very faster. 2) API contains reusable Components & Layouts that developers can directly use in their projects. 3) Just include project JAR file in your existing project then import and use all features (refer JavaWizardDevelopmentDocumentation) * Don't worry about Java's complex layouts, just pass your components as parameters to our "MyLayout" class and we'll do it for you. * New & pre-aligned UI components like... -
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dna-bison
Bisulfite alignment On Nodes of a cluster
Bison allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads. It can align both directional and non-directional libraries and uses bowtie2. Multiple compute nodes are not absolutely required, but will make the alignment process faster. Further details available on the Wiki page. Help also available on SEQanswers (http://seqanswers.com/forums/showthread.php? -
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notepas
Advanced multiplatform text editor for developers
Notepas is a fast native multiplatform text editor written in Lazarus and can be compiled for multiple platforms and widget sets using the advanced native Free Pascal Compiler. Aimed towards developers it is equipped with some functions usually not found in other text editors and introduces a couple of new exclusive features. -
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This program is a fork of ClovisGrid (https://sourceforge.net/projects/clovisgrid/) This program runs a simple grid that displays over SWTOR to allow you to more easily align your GUI with the new patch 1.2 interface editor. For questions or support, please contact me using the information provided below: CrazyAmbro (Black Vulkars US) / The Bastion
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New version was released! Visit https://github.com/jsnjack/simpleblogger to download Simple Blogger is a small and very easy to use application that enables you to quickly write and publish a new post of your blog. Available in Windows and Linux. Simple Blogger has written on Python with wxPython.
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RDP FrameBot is a frameshift correction and nearest neighbor classification tool for use with high-throughput amplicon sequencing. It uses a dynamic programming algorithm to align each query DNA sequence against a set of target protein sequences, produces frameshift-corrected protein and DNA sequences and an optimal global or local protein alignment. It also helps filter out non-target reads. The online version of FrameBot is available on http://fungene.cme.msu.edu/FunGenePipeline, tutorial http://rdp.cme.msu.edu/tutorials/framebot/RDPtutorial_FRAMEBOT.html. ...
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calc2booktab.latex
Script for OpenOffice/LibreOffice to convert tables to Latex-Code
UPDATE: The project was moved to github (https://github.com/schober-ch/calc2booktab). The soruceforge page won't get any bugfixes, please use the github repo if you want to try this macro. -------------------------------------------------------------------------- A Python extension for OpenOffice/LibreOffice to convert selected cells to LaTeX-Code. Its similar to Calc2Latex, but typographic formatting is more advanced (numeric columns, dcolumn-package, booktab-package) Script is... -
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FineSplice
Enhanced splice junction detection and estimation from RNA-Seq data
FineSplice is a Python wrapper to TopHat2 geared towards a reliable identification of expressed exon junctions from RNA-Seq data, at enhanced detection precision with small loss in sensitivity. Following alignment with TopHat2 using known transcript annotations, FineSplice takes as input the resulting BAM file and outputs a confident set of expressed splice junctions with the corresponding read counts. Potential false positives arising from spurious alignments are filtered out via a... -
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GLProbs
GLProbs: Aligning multiple sequences adaptively
GLProbs is a simple and effective approach to improve the accuracy of multiple sequence alignment. We use a natural measure to estimate the similarity of the input sequences, and based on this measure, we align the input sequences differently. To test the effectiveness of this approach, we have implemented a multiple sequence alignment tool called GLProbs and compared its performance with a dozen leading alignment tools on three benchmark alignment databases, and GLProbs’s alignments has the best scores in almost all testings. We have also evaluated the practicability of the alignments of GLProbs by applying the tool to three biological applications, namely phylogenetic trees construction, protein secondary structure prediction and the detection of high risk members for cervical cancer in the HPV-E6 family, and the results are very encouraging. -
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blastplot
A simple and easy to use perl package to plot blast output results
...Read-based BLAST analysis of NGS data is a common procedure especially in the case of metagenomic samples. However, coverage is usually not enough to allow for de novo assembly. This type of read-based analysis often creates the question of how a set of reads that align to the same sequence is distributed. The same question applies to preparation of primers or probes for microarray experiments. We have created BLASTPLOT, a PERL module to quickly plot the BLAST results from short sequences (primers, probes, reads) against reference targets. BLASTPLOT is a simple to use PERL module that allows the generation of PNG graphs for all the reference sequences associated with a BLAST result set. ... -
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A free computer-aided translation / computer-assisted translation (CAT) tool to align and converter bitext into TMX translation memory format to be used in other CAT tools by translators and other language professionals.
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SOAPindel2
SOAPindel2 focusing on calling indels from the next-generation p
Requirements SOAPindel2 needs two input data sources: The reference sequence file used to align the reads. It must be in Fasta format. The files with read-alignments. SOAPindel2 accepts only Indexed BAM formats as input. Users can use the tools/soap2sam.cc to convert SOAP format to SAM format and use samtools convert SAM to indexed BAM. SOAPindel2 can guess the library insert sizes by itself. Sequencing platform:Theoretically, SOAPindel2 is designed for all paired-end sequencing data because it doesn’t consider any qualities for now. ... -
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Qudaich
Performs local sequence alignment for NGS data
...Qudaich is flexible and its algorithmic structure imposes no restriction on the absolute limit of the acceptable read length, but the current version of qudaich allow read length <2000 bp. Qudaich can be used to align DNA, translated DNA and protein sequences. -
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iAstroDroid
Automated astrophotography on Android
iAstroDroid is a world first solution for controlling the autoguider, CCD, DSLR, and mount for astrophotography on Android devices. iAstroDroid run on a parallel OS (Chroot) on an Android device. A user can control all devices via a web browser on Android. Requirements and supported devices. 1. Autoguider: QHY5 or QHY6 2. CCD: QHY8L 3. DSLR: Canon or Nikon DSLR 4. USB serial adapter (FTDI232) for controlling a DSLR camera shutter and a serial shutter... -
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tisa - Tab Indent Space Align
A program that will correct both indentation and alignment.
