http://www.ub.edu/dnasp/ - DnaSP is a software package for a comprehensive analysis of DNA polymorphism data. Version 5 implements a number of new features and analytical methods allowing extensive DNA polymorphism analyses on large datasets. Among other features, the newly...
help.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...
github.com - methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods such as Agilent...
drive5.com - USEARCH >Extreme high-throughput sequence analysis. Orders of magnitude faster than BLAST. MUSCLE >Multiple sequence alignment. Faster and more accurate than CLUSTALW.
UPARSE >OTU clustering for 16S and other marker genes....
www.sequenceontology.org - We have developed the Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome. We envisage its use during annotation jamborees, genome comparison and for use by developers...
academic.oup.com - Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the...
github.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...
www.phrap.org - Supports Illumina, 454, other Next-Gen and Sanger Reads and allows mixtures of these read types
Consed includes BamScape which can view bam files with unlimited numbers of reads. BamScape can bring up consed to edit reads and the reference sequence...
