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www.cbcb.umd.edu - Metagenomics sequencing projects collect samples of DNA from uncharacterized environments that may contain hundreds or even thousands of species. One of the main challenges in analyzing a metagenome is phylogenetic classification of raw sequence...

www.csd.uwo.ca - E-MEM is a C++/OpenMP program designed to efficiently compute MEMs between large genomes. See the README file for instructions on how to use E-MEM. E-MEM source code The source code can be downloaded here. If you use E-MEM, please...

chibba.agtec.uga.edu - MCscan is a computer program that can simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors. This is the toolset for generating the synteny correspondences...

ics.hutton.ac.uk - Strudel is our graphical tool for visualizing genetic and physical maps of genomes for comparative purposes. The application aims to let the user examine their data at a variety of different levels of resolution, from entire maps to individual...

ratt.sourceforge.net - RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome. It was first developed to transfer annotations between different genome assembly versions. However, it can also transfer annotations between...

The genome assemblers generally take a file of short sequence reads and a file of quality-value as the input. Since the quality-value file for the high throughput short reads is usually highly memory-intensive, only a few assemblers, best suited for...

www.jcvi.org - CABOG (Celera Assembler with Best Overlap Graph) is scientific software for DNA research. CABOG has been a critical component of many genome sequencing projects. CABOG operates on small genomes such as bacterial as well as large genomes such as...

kissplice.prabi.fr - KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler that allows to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number...

crossmap.sourceforge.net - CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10...

urgi.versailles.inra.fr - We advise to run first the TEdenovo pipeline but it is not compulsory. We suppose you begin by running the TEannot pipeline on the example provided in the directory "db/" rather than directly on your own genomic sequences. Thus, from now on, the...