Search Results for "alignment" - Page 16
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Showing 492 open source projects for "alignment"
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Normalize.css
A modern alternative to CSS resets
...Rather than a “hard reset” that zeroes everything, it preserves sensible defaults for elements while fixing inconsistencies and edge cases that vary between engines. The project documents why each rule exists, targeting real-world quirks such as form control alignment, typographic defaults, and HTML5 element rendering. It is deliberately minimal and stable, making it a safe foundation for both custom design systems and heavyweight frameworks. Because it normalizes only what’s necessary, it plays well with component libraries and avoids surprising overrides that can lead to fragile CSS. Teams adopt it to reduce cross-browser bugs, speed up layout work, and start with predictable typography, spacing, and element behavior. -
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PhyloTreePruner
A nifty Java program for pruning phylogenetic trees.
...These trees are then provided to PhyloTreePruner which checks them for evidence of paralogy (i.e., multiple sequences from the same taxon that do not form a clade), trims suspected paralogs from the data matrix, and generates a new alignment containing only sequences inferred as orthologs. Preliminary tests of PhyloTreePruner on a variety of datasets indicate that this method successfully removes paralogous sequences and thus should help improve the accuracy of inferred species trees. -
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Qudaich
Performs local sequence alignment for NGS data
Qudaich (queries and unique database alignment inferred by clustering homologs) is a software package for aligning sequences. Qudaich generates the pairwise local alignments between a query dataset against a database. The main design purpose of qudaich is to focus on datasets from next generation sequencing. These the datasets generally have hundreds of thousand sequences or more, and so, the input database should contain large number of sequences. -
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Vanator-CVR
A metagenomics & virus discovery pipeline
Vanator (Virus Alignment, de Novo Assembly and Taxonomy On Reads) is a Perl pipeline utilising a large variety of common alignment, assembly and analysis tools to assess the metagenomic profiles of Illumina deep sequencing samples. The emphasis is on the discovery of novel viruses in clinical and environmental samples. The philosophy behind Vanator is described by Jarrett et al (2013) http://www.ncbi.nlm.nih.gov/pubmed/23296970 -
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ProGraphMSA
Graph-based multiple sequence alignment
...Further, we account for variations in the substitution pattern by using estimated amino acid frequencies and by implementing context-specific profiles as in CS-Blast. The latest versions of ProGraphMSA include and extension to the alignment model to support tandem repeat unit insertions and deletions. -
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LaTeX Table Creator
Simple Cross-platform LaTeX table creator with a GUI and console app.
...Uses the output of standard spreadsheet software (MS Office, Libre Office, Gnumeric) to create a LaTeX tabular object that contains the specified data. Automatically detects the size of the table. The user can optionaly specify some basic formatting information, such as alignment, borders, bold headings. The user can also select if the input is tab (default) or comma delimited and can disable the tabular structure in the output. This allows the output to b easily appended to an existing table. This application is intended for importing "large" amounts of data into a LaTeX table. It is not intended to make fancy formatting easier. ... -
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Component for structural analysis (graph-based concept and entity linking, segmentation and alignment of comparable texts)
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ContigScape
Cytoscape plugin for visualizing contig relationships
ContigScape is a Cytoscape plugin which utilize ace and mate-paired alignment for visualizing the relationship between contigs. -
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Biscap and cfdr
Scripts for post-alignment snp-calling and verification
A script for determining homozygous and heterozygous positions from an alignment using binomial probabilities from a predicted error rate (BiSCaP) and a method to benchmark the accuracy of this and other alignment/SNP-calling methods (cFDR) -
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MapPSO is a tool for Ontology Alignment, which uses Discrete Particle Swarm Optimisation. A particle swarm is used to search for the optimal alignment. The algorithm is massively parallel and adapts naturally on parallel architectures.
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Onco-STS
A web-based Laboratory Information Management System
Onco-STS is a web-based Laboratory Information Management System for sample and analysis tracking in oncogenomic experiments. The systematic sequencing and analysis of tumour samples, as well other oncogenomic experiments, necessitates the tracking of relevant sample information throughout the investigative process. These meta-data of the sequencing and analysis procedures include information about the samples and projects as well as the sequencing centers, platforms, data locations,... -
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Eskil is a graphical tool to view the differences between files and directories. It supports version management and patch files and has various preprocessing and alignment options to improve the display of tricky diffs.
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SAMMate
RNA-Seq Transcriptome Assembly and Analysis
...The software allows users to accurately estimate gene expression and isoform expression scores using short reads to generate wiggle files for visualization in UCSC genome browser and an alignment statistics report. -
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Topic Model Alignment
Aligns two LDA topic models
This script aligns two topic models produced by MALLET (http://mallet.cs.umass.edu/) Reciprocal topic pairs are reported with JS divergence measure. Reciprocal pair (i,j) is defined when the distance of topic i from the first model (M1) and topic j from the second model (M2) is minimal for all pairs (i,k) for k in M2 and (l,j) for l in M1 (best match for both topics). This is useful for: 1. Qualitatively comparing different modeling parameters or algorithms 2. Identifying stable... -
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NeedlemanWunsch
Fast global sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align Global optimal sequence alignment using the Needleman-Wunsch algorithm. Aligns DNA, RNA, protein sequence and more! See our sister project local alignment using Smith-Waterman: http://sourceforge.net/projects/smithwaterman/ -
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tisa - Tab Indent Space Align
A program that will correct both indentation and alignment.
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MolBioLib
C++11 framework for rapid develop and deploy of bioinformatic tasks.
...A central relational-database-like Table class is a flexible and powerful object to intuitively represent and work with a wide variety of tabular datasets, ranging from alignment data to annotations. MolBioLib includes programs to perform a wide variety of analysis tasks such as computing read coverage, annotating genomic intervals, and novel peak calling with a wavelet algorithm. While MolBioLib was designed primarily for bioinformatics purposes, much of its functionality is applicable to a wide range of problems. ... -
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Ferox
Ferox - Sequence Alignment with Fuzzy K-mers
Ferox is a DNA sequence alignment application that uses fuzzy k-mers to quickly and accurately align sets of sequence reads against a reference genome. Ferox can also be used to align whole genomes. The seeding mechanism used by Ferox is highly configurable, allowing custom fuzzy seeds to be created declaratively in an XML configuration file. -
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Altrans
Quantification of Splicing Events
Altrans is a method for the relative quantification of splicing events. It requires a BAM alignment file from an RNA-seq experiment and an annotation file in GTF format detailing the location of the exons in the genome. It uses paired end reads where one mate maps to one exon and the other mate to a different exon and/or split reads spanning exon exon junctions to count “links” between two exons. When there are overlapping exons, these are grouped into “exon groups” and unique portions of each exon in an exon group are identified which are used when assigning reads to an exon. ... -
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Mirroring co-evolving trees
Mirroring co-evolving trees in the light of their topologies
...In this article, we devise an efficient deterministic algorithm which directly maximizes the similarity between two leaf labeled trees with edge lengths, obtaining a score-optimal alignment of the two trees in question. -
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SeqHunter2
a stand-alone bioinformatics software for querying genome sequences
...It is programmed with the following functions: 1) collect and manage local sequence databases; 2) run blast search by using a batch of sequences and with abundant output formats; 3) extract sequences by a set of IDs or coordinates; 4) generate sequences alignment; 5) edit sequence and translate nucleotide to proteins; 6) browse genome and search genes; 7) collect resource items and link to the website. The full version collects all available oomycete plant pathogens genome sequences and information of research related resource, while the lite version is flexible for non-oomycete users to collected the data they are interested. -
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BioWord
A Microsoft Word add-in for biological sequence manipulation
BioWord, a Microsoft Word add-in, allows instant access to most sequence manipulation needs, such as reverse-complementing, translating or FASTA formatting, and features a full suite of sequence search methods, pair-wise alignment and motif discovery. -
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SmithWaterman
Fast local sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align An implementation of the Smith-Waterman local sequence alignment algorithm. See our sister project global alignment using Needleman-Wunsch: http://sourceforge.net/projects/needlemanwunsch/ -
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Click Through Image Overlay
Used to overlay an image with a click through window
Ordinarily used for tracing one image to an editor for art and drawings, but can also be used from alignment of objects to visual disabilities that need temporary hue changes that can be quickly removed. the image window is click through so clicking on on it results to clicking on what's behind it. the image window is movable and re-sizable by checking the lock to move. also supports web cam overlay and a basic 10pt black on white text overlay.