Jit
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Genome Simulation with SLiM and msprime
By BioStar 498 days agoSLiM and msprime are valuable tools for genome simulation, each serving distinct but complementary purposes in population genetics research. By leveraging the strengths of both simulators with slendr, researchers can conduct robust and efficient...mafTools
By Radha Agarkar 3674 days agogithub.com - Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.Mercator: Multiple Whole-Genome Orthology Map Construction
By Jit 2215 days agowww.biostat.wisc.edu - Whole-genome homology maps attempt to identify the evolutionary relationships between and within multiple genomes. The term "syntenic" is often used to describe regions of multiple genomes that are believed to have evolved from the same region in an...Reference-free prediction of rearrangement breakpoint reads
By Neel 3019 days agocode.google.com - lideSort-BPR ( b reak p oint r eads) is based on a fast algorithm for all-against-all comparisons of short reads and theoretical analyses of the number of neighboring reads. When applied to a dataset with a sequencing...GenBank release 257.0 is now available!
By Neel 1025 days agoGenBank release 257.0 is now available! This release has 25.10 trillion bases and 3.69 billion records.pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
By Jit 2942 days agogithub.com - pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file...RopeBWT2: Incremental construction of FM-index for DNA sequences
By Rahul Nayak 2788 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...UPhO: Scripts for homology and orthology assessment from genomic sequences.
By BioStar 2707 days agogithub.com - UPhO finds orthologs with and without inparalogs from input gene family trees. Refer to the Documentation.pdf for more detailed explanations on its usage, installation and dependencies. Type UPhO.py -h for help. The only input requierement for UPhO...NucDiff: In-depth characterization and annotation of differences between two sets of DNA sequences
By Jit 2230 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...Common methods to discover tandem repeats
By BioStar 1192 days agoTandem repeats are DNA sequences that are repeated in a contiguous manner in the genome.
