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Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the...
By Rahul Nayak 1822 days agopypi.org - The Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees (although clustering trees or any other tree-like data structure are also...netGO: R-Shiny package for network-integrated pathway enrichment analysis
By Jit 1745 days agogithub.com - netGO is an R/Shiny package for network-integrated pathway enrichment analysis.netGO provides user-interactive visualization of enrichment analysis results and related networks. Currently, netGO supports analysis for four species...
Sample bandage input file for visual analysis
By Jit 1416 days agoSample bandage input file for visual analysis ...Kmer: a suite of tools for DNA sequence analysis
By BioStar 1192 days agohelp.rc.ufl.edu - More at https://help.rc.ufl.edu/doc/Kmer This also includes: A2Amapper: ATAC, Assembly to Assembly Comparision tool: Comparative mapping between two genome assemblies (same species), or between two different genomes (cross...InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams
By Jit 877 days agowww.interactivenn.net - InteractiVenn, a more flexible tool for interacting with Venn diagrams including up to six sets. It offers a clean interface for Venn diagram construction and enables analysis of set unions while preserving the shape of the diagram. Set unions are...pipesnake: bioinformatics best-practice analysis pipeline for phylogenomic reconstruction
By LEGE 275 days agogithub.com - ausarg/pipesnake is a bioinformatics best-practice analysis pipeline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data. The pipeline is built using Nextflow, a workflow tool to run tasks across...GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
By Jit 2725 days agogithub.com - GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.htmlFeatures Mapping position agnostic to alignment parameters. ...MashMap: a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to...
By Jit 2537 days ago Comments (1)github.com - MashMap is a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s). It maps a query sequence against a reference region if and only if its estimated alignment identity is above a specified threshold. It...ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.
By Seema Singh 2398 days agogithub.com - ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set. Detail paper...TAREAN: A computational tool for identification and characterization of satellite DNA from...
By Surabhi Chaudhary 2383 days agobitbucket.org - TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their...
