Search Results for "multiple sequence alignment" - Page 8
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Showing 231 open source projects for "multiple sequence alignment"
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Multiple optima
Scripts used to detect multiple optima of likelihood on real data.
R scripts and sequence data used in the paper "Multiple local maxima for likelihoods of phylogenetic trees constructed from biological data." by McComish BJ, Schliep KP and Penny D (submitted to Systematic Biology). -
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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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Bowling Score
Simple Java project to compute the bowling score
A simple Java project meant to compute the score of a bowling game. Currently implemented: - src/ao.bowling: architecture for the bowling game (a Game can be played by multiple Players, each Player has 10 Frames in which to knock down the pins within 1-3 Throws) - test/ao.bowling: JUnit test cases for a few typical scenarios TODO: - parse&sanitize user input (sequence of numbers representing number of pins knocked down at each throw) - simple swing interface where user inserts data and gets the score - documentation -
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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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multipsq
Analysis of pyrograms form multiplex pyrosequencing experiments
...The assays can be designed using the software mpsqed available from https://sourceforge.net/projects/mpsqed/ Pyrosequencing can be applied for Single-Nucleotide-Polymorphism (SNP)-based pathogen typing or for providing sequence information of short DNA stretches. However, for some pathogens molecular typing cannot be performed relying on a single SNP or short sequence stretch, necessitating the consideration of several genomic regions. A promising rapid approach is the simultaneous application of multiple sequencing primers, called multiplex pyrosequencing. ... -
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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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Firefly UML
A free, easy-to-use and user-friendly Java-based UML editor.
Firefly UML is a 100% pure Java application designed to create and edit UML conform diagrams. With class diagrams, sequence and instance diagrams, Firefly UML provides a solid selection from the vast range of existing UML diagram types. Firefly UML is really easy to learn as it provides you multiple ways of access to the same function - be it mouse action, hotkey, context menu or toolbar icon. And the best thing is: once you have learned how to handle one type of diagram, you also have learned how to deal with the other diagram types, because they all follow the exactly same user interaction patterns. ... -
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Pontos
Pontos calculates distance matrices from DNA sequence alignments.
Pontos is an easy-to-use, graphical Java program for the calculation of uncorrected distance (or similarity) matrices from DNA sequence alignments in PHYLIP format. It also creates "difference" alignments from regular ones (and vice-versa). It can handle gaps and ambiguities in different ways. Gaps can be: - all used; - all ignored; - ignored only at the ends of the sequences, in a pairwise manner; - ignored only at the ends, but now globally (in effect trimming the whole alignment to the farthest sequences from the ends). ... -
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JFinisher
JFinisher is software for alignment, editing and manipulation DNA seqs
JFinisher is software for alignment, editing and manipulation of biological sequences. It aims to assist in the finishing of genome assembly. Starting from a reference sequence, the program align contigs using Smith-Waterman local alignment algoritm with auxiliary methods, allowing management of the alignments generated. It has graphical interface for manipulation and visualization of the actions, uniting features that help in editing the sequences. -
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We will develop a Sequence alignment LIMS System to integrate multiple NGS(Next Generation Sequencing) System. The system will be developed, based on EJB technologies.
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ZORRO is a probabilistic masking program that assigns confidence scores to each column in a multiple seqeunce alignment. These scores can then be used to account for alignment accuracy in phylogenetic inference pipelines.
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BFAST facilitates the fast and accurate mapping of short reads to reference sequences, where mapping billions of short reads with variants is of utmost importance.
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MultiArtemis imports BLAST output (with -m 8 specified) into Artemis genome browser (www.sanger.ac.uk) entries. It is designed for mapping multiple contigs or scaffolds back to reference sequence and view.
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A peak caller for ChIP-Seq experiments that robustly handles short reads with *multiple* possible mappings. Releases are hosted here, but development source code is available at https://github.com/jakebiesinger/AREM. A Google group has been set up to help with questions from the community and for announcements of new builds. http://groups.google.com/group/arem-announcements
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3D Genome Tuner draws circular genome map and enables viewing multi-genomes in 3D context. It also provides genome analysis and sequence alignment, making it a powerful tool in genome studies and demonstrations.
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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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MultiBamView was developed on BamView for displaying multiple Bam files simultaneously. It is useful in comparing several runs mapped to the same reference sequence, finding shared or unique mutations.
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IMPACT
Integrated Multiprogram Platform for Analyses in ConTest
Graphical User Interface for a software used to assess adaptive evolution in protein-coding genes. Makes use of several known bioinformatics software. IMPACT is free software, targeted to the scientific community. Maldonado E, Dutheil JY, da Fonseca RR, Vasconcelos V, Antunes A (2011) IMPACT: Integrated Multiprogram Platform for Analyses in ConTest. Journal of Heredity, 102 (3): 366-369. doi: https://doi.org/10.1093/jhered/esr003 -
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VELMA stands for Visualization & Exploration of Large Multiple sequence Alignments. VELMA is a Java tool for visualizing alignments of large numbers of biological sequences that exceed the capabilities of existing software.
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This software computes likelihoods for infinitely-many-sites sequence data under multiple merger coalescents. The likelihood can be computed exactly or approximated via importance sampling.
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NGS-Cleaner is an application that provides cleaning of FASTQ/A formatted large DNA sequence files containing multiple short-reads sequences provided by Next Generation Sequencing platforms.
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C++ library for protein sequence profile to profile alignment. Implementing numerous known alignment variants in a flexible and manageable architecture.
