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Neel on Fix rewritable error of ELGG ! (924 days ago): sudo systemctl restart apache2 Now, create...- Shruti Paniwala on LASTZ (3065 days ago): The latest relase of LastZ at http://www.bx.psu.edu/~rsharris/lastz/newer/
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MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction
By Abhi 240 days agogithub.com - MIKE (MinHash-based k-mer algorithm). This algorithm is designed for the swift calculation of the Jaccard coefficient directly from raw sequencing reads and enables the construction of phylogenetic trees based on the resultant Jaccard...UniAligner: a parameter-free framework for fast sequence alignment
By Abhi 270 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,...PhyloHerb: A high‐throughput phylogenomic pipeline for processing genome skimming data
By Abhi 455 days agogithub.com - Phylogenomic Analysis Pipeline for Herbarium Specimens What is PhyloHerb: PhyloHerb is a wrapper program to process genome skimming data collected from plant materials. The outcomes include the plastid genome (plastome) assemblies,...MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
By Abhi 456 days agogithub.com - MitoHiFi v3.2 is a python pipeline distributed under MIT License ! MitoHiFi was first developed to assemble the mitogenomes for a wide range of species in the Darwin Tree of Life Project...Biostats book !
By Abhi 478 days agopractical-stats-med-r.netlify.app - https://practical-stats-med-r.netlify.app/Metabuli 분리 improves metagenomic read classification
By Abhi 549 days agogithub.com - Metabuli 분리 improves metagenomic read classification through metamers, DNA-AA k-mers, to be sensitive and specific, recovering 99% and 98% of DNA or AA classifiers. Metabuli is metagenomic classifier that jointly analyze both DNA and amino...homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes
By Abhi 549 days agogithub.com - This tutorial describes the usage of homologizer to phase gene copies into polyploid subgenomes. The tutorial is an abbreviated version of a soon-to-be published paper in Methods in Molecular Biology. Please see that paper for many more...OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes
By Abhi 582 days agoorthovenn3.bioinfotoolkits.net - OrthoVenn3 is a powerful tool for comparative genomics analysis, used as a web server for full genome comparisons, annotation, and evolutionary analysis of orthologous clusters across multiple species. It has already been used by thousands of users...JBrowse 2: a modular genome browser with views of synteny and structural variation
By Abhi 588 days agogithub.com - igvjs - a create-react-app with igv package from npm installed. the igv.js is instrumented to output "DONE" to the console when finished, and to have an increased fetchSizeLimit (which is otherwise git in CRAM longread tests) jb2-web - stock...genomenotebook
By Abhi 594 days agodbikard.github.io - https://dbikard.github.io/genomenotebook/ Install pip install genomenotebook How to use Create a simple genome browser with a search bar. The sequence appears when zooming in. import genomenotebook as gn g=gn.GenomeBrowser(genome_path,...
