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MSAProbs - Parallel and accurate multiple sequence alignment
By Neel 1993 days agomsaprobs.sourceforge.net - MSAProbs is a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior...VG: variation graph data structures, interchange formats, alignment, genotyping, and variant...
By Jit 1791 days agogithub.com - Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg) is composed of: nodes, which are labeled by sequences and ids edges, which connect two nodes via either of...UniAligner: a parameter-free framework for fast sequence alignment
By Abhi 289 days agogithub.com - UniAligner (formerly, TandemAligner) is the first parameter-free algorithm for sequence alignment that introduces a sequence-dependent alignment scoring that automatically changes for any pair of compared sequences. Classical alignment approaches,...Alvis: a tool for contig and read ALignment VISualisation and chimera detection
By LEGE 229 days agogithub.com - Alvis, a simple command line tool that can generate visualisations for a number of common alignment analysis tasks. Alvis is a fast and portable tool that accepts input in a variety of alignment formats and will output production ready vector...A fast package to parse BLAST
By Jitendra Narayan 4121 days ago, managBlaSTorage: a fast package to parsee and store BLAST resultsBLAST Ring Image Generator (BRIG)
By Anjana 3006 days agobrig.sourceforge.net - BRIG is a free cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. The application is available at:...New Layout for BLAST ftp Database Site
By Jit 1797 days ago Comments (1)New Layout for BLAST ftp Database SiteCircoletto: visualizing sequence similarity with Circos
By Jit 2508 days agotools.bat.infspire.org - Circoletto, an online visualization tool based on Circos, which provides a fast, aesthetically pleasing and informative overview of sequence similarity search results. Online version and downloadable software package for offline use (source code in...BEAP: Blast Extension and Assembly Program
By Shruti Paniwala 2387 days agowww.animalgenome.org - The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide databases in an attempt to obtain all sequences that...
