Whole genome alignment software tools | High-throughput sequencing data analysis
The huge number of genomes sequenced every day makes the development of effective comparison and alignment tools ever more urgent. Indeed, many microbiological applications rely directly on genome alignments, for instance micro-diversity and phylogenomic analysis of bacterial strains, assembly and annotation procedures for datasets of closely-related genomes or prediction of maintenance motifs in non-model species.
Offers a platform supplying multiple methods for aligning genomic sequences. LAGAN is a toolkit of algorithms composed of three main features: (i) LAGAN, that can be applied for genomic comparison of distantly related organisms; (ii) Multi-LAGAN, which is a multiple aligner based on progressive alignment integrating approaches for scoring alignment with affine gaps and; (iii) Shuffle-LAGAN, a glocal aligner with the aim of enabling the aligning of long genomic sequences.
Calculates in silico the extent of identity between two genomes. JSpeciesWS is able to determine overall genome relatedness indices (OGRI). It allows rapid comparisons against the reference database offered by the tool, providing a list of the most similar genomes based on their resulting Tetra-nucleotide signature correlation index. This database is composed of NCBI’s genomic sequence data and includes all primary submissions of assembled genome sequences and their associated annotation data.
Compares eukaryotic genomes at varying evolutionary distances. MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system.
Leverages years of customer feedback and development for analysis tools for SOLiD system data, to enable faster translation of next-generation data to biologically meaningful results. Designed to match the accuracy of the next generation 5500 Genetic Analyzers with Exact Call Chemistry (ECC), LifeScope streamlines your data analysis.
Builds multiple genome alignments from large-scale evolutionary events including rearrangement and inversion. Mauve is a standalone application dedicated to the reconstruction of positional homology multiple genome alignments. This program is a combination of three algorithms: (i) a sum-of-pairs breakpoint score; (ii) a greedy heuristic and (iii) a homology hidden Markov model.
Processes alignments of user-submitted sequences. mVISTA performs pairwise alignments of DNA sequences up to megabases long from two and more species. This software allows visualization of alignments with annotations which display global sequence alignments of genomic sequences from different species. It can also assess percentage identity and length cutoffs for identifying a level of active non-coding conservation by comparing all pairwise sequence alignments of three or more species.
Enables efficient microbial core genome alignment and single-nucleotide polymorphisms (SNP) detection. Parsnp utilizes a Directed Acyclic Graph (DAG) data structure, called a Compressed Suffix Graph (CSG), to index the reference genome for efficient identification of multi- maximal unique matches (MUMs). The software is suited for outbreak analyses of infectious diseases and offers a highly efficient method for aligning the core genome of thousands of closely related species. Besides, the tool is a part from the Harvest suite.