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DnaSP: DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms
By Neel 2139 days agohttp://www.ub.edu/dnasp/ - DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms using data from a single locus (a multiple sequence aligned -MSA data), or from several loci (a Multiple-MSA data, such as formats generated by some...FGENESH - Program for predicting multiple genes in genomic DNA sequences
By BioStar 2846 days agowww.softberry.com - FGENESH is the fastest (50-100 times faster than GenScan) and most accurate gene finder available - see the figure and the table below. In recent rice genome sequencing projects, it was cited "the most successful (gene finding) program (Yu et...GeneOverlap: An R package to test and visualize gene overlaps
By Jit 2838 days agobioconductor.org - Overlapping gene lists can reveal biological meanings and may lead to novel hypotheses. For example, histone modification is an important cellular mechanism that can pack and re-pack chromatin. By making the chromatin structure more dense or loose,...Termal: a fast and interactive terminal-based viewer for multiple sequence alignments
By LEGE 377 days agogithub.com - termal, a fast, interactive, terminal-based viewer for multiple sequence alignments (MSAs), designed for use on remote systems such as high-performance computing (HPC)...SMASH: An alignment-free tool to find and visualise rearrangements between pairs of DNA sequences
By Jit 3210 days agogithub.com - SMASH is a completely alignment-free method to find and visualise rearrangements between pairs of DNA sequences. The detection is based on relative compression, namely using a FCM, also known as Markov model, of high context order (typically...D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way
By Jit 3038 days agodgenies.toulouse.inra.fr - D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation. We use minimap...Miropeats: discovers regions of sequence similarity amongst any set of DNA sequences
By Poonam Mahapatra 2596 days agowww.littlest.co.uk - Miropeats discovers regions of sequence similarity amongst any set of DNA sequences and then presents this similarity information graphically. Sequence similarity searching is a very general tool that forms the basis of many different biological...MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
By Jit 2786 days agobioweb.supagro.inra.fr - MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containing...Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map
By Jit 2399 days agogithub.com - A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. (https://github.com/vgteam/vg) Link to working demo:...Pacman
By Rahul Nayak 4248 days agoThe pacman package is an R package management tool that combines the functionality of base library related functions into intuitively named functions.
