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Laj: viewing and manipulating the output from pairwise alignment programs
By Abhimanyu Singh 3295 days agowww.bx.psu.edu - Laj is a tool for viewing and manipulating the output from pairwise alignment programs such as blastz. It can display interactive dotplot, pip, and text representations of the alignments, a diagram showing the locations of exons and repeats, and...DIAL
By Abhimanyu Singh 3295 days agowww.bx.psu.edu - A computational pipeline for identifying single-base substitutions between two closely related genomes without the help of a reference genome. DIAL works even when the depth of coverage is insufficient for de novo assembly, and it can be extended to...splitbam: splits a BAM by chromosomes
By Jit 3296 days agocode.google.com - splitbam splits a BAM by chromosomes. Using the reference sequence dictionary (*.dict), it also creates some empty BAM files if no sam record was found for a chromosome. A pair of 'mock' SAM-Records can also be added to those empty BAMs to...ALPHA: A Toolkit for Automated Local Phylogenomic Analyses
By Jit 2910 days agogithub.com - Automated Local Phylogenomic Analyses, or ALPHA, is a python-based application that provides an intuitive user interface for phylogenetic analyses and data visualization. It has four distinct modes that are useful for different types of phylogenetic...Multi-metagenome assembly
By Radha Agarkar 3293 days agogithub.com - This project contains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in: Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomesMads...QuartataWeb: user-friendly server developed for polypharmacological and chemogenomics analyses.
By Neel 2168 days agoquartata.csb.pitt.edu - Data on protein-drug and protein-chemical interactions are rapidly accumulating in databases such as DrugBank and STITCH. These data usually reflect observed interactions, while the lack of data for a given protein-drug/chemical pair...CONCOCT: Clustering cONtigs with COverage and ComposiTion
By Jit 3290 days agogithub.com - A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Warning! This software is to be considered under development. Functionality and the...SeqMule: Automated human exome/genome variants detection
By Abhimanyu Singh 3289 days agoseqmule.openbioinformatics.org - SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its...Five unique traits of effective computational biologist
By Jitendra Narayan 4624 days ago Comments (3)Traits of biological programmers
