Jit
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rHAT: a seed-and-extension-based noisy long read alignment tool
By Abhimanyu Singh 2724 days agogithub.com - rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT)...NucDiff: In-depth characterization and annotation of differences between two sets of DNA sequences
By Jit 2134 days agogithub.com - NucDiff locates and categorizes differences between two closely related nucleotide sequences. It is able to deal with very fragmented genomes, structural rearrangements and various local differences. These features make NucDiff to be perfectly...SVbyEye: R Package to visualize alignments between two or multiple DNA sequences
By LEGE 538 days agogithub.com - R Package to visualize alignments between two or multiple DNA sequences includinga number of functionalities to facilitate processing of alignments in PAF format. SVbyEye, an open-source R package to visualize and annotate sequence-to-sequence...COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 3015 days agoftp.genomics.org.cn - An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE...MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
By Jit 2576 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...Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment
By Poonam Mahapatra 2837 days agomolevol.cmima.csic.es - Gblocks eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis. This server implements the most important features of the Gblocks program to make its...A web-based tool for sequence alignment statistics and innovative visualization
By BioStar 704 days agobioinformatics.um6p.ma - AlignStatPlot, a new R package and online tool that is well-documented and easy-to usefor MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analy-ses on sequencing data and generates new visualisation methods for MSA...Alvis: a tool for contig and read ALignment VISualisation and chimera detection
By LEGE 670 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...RopeBWT2: Incremental construction of FM-index for DNA sequences
By Rahul Nayak 2692 days agogithub.com - RopeBWT2 is an tool for constructing the FM-index for a collection of DNA sequences. It works by incrementally inserting one or multiple sequences into an existing pseudo-BWT position by position, starting from the end of the sequences. This...Common methods to discover tandem repeats
By BioStar 1096 days agoTandem repeats are DNA sequences that are repeated in a contiguous manner in the genome.
