MUMmer4: A fast and versatile genome alignment system
...mer4 can now work with input sequences of any biologically realistic length. We show that as a result of these enhancements, the nucmer program in MUMmer4 is easily able to...2296 days ago
PhyloGrapher - Graph Visualization Tool
PhyloGrapher is a program designed to visualize and study evolutionary relationships within families of homologous genes or proteins (elements). PhyloGrapher is a dr...2264 days ago
HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single referenc...2203 days ago
CrossMap: a program for convenient conversion of genome coordinates
CrossMap is a program for convenient conversion of genome coordinates (or annotation files) betw...designed to liftover genome coordinates between assemblies. It’s not a program for aligning sequences to ref...2179 days ago
Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment
...sis. This server implements the most important features of the Gblocks program to make its use as simple as...in most of the cases. Other options can be changed in the stand-alone program. You can see here an exa...2177 days ago
MCMCTREE: a phylogenetic program for Bayesian estimation of species divergence times
MCMCTREE is a phylogenetic program for Bayesian estimation of species divergence times using soft fossil constraints under various molecular clock models. This is part of the&nbs...2177 days ago
BEAP: Blast Extension and Assembly Program
The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide datab...2169 days ago
npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbi...2169 days ago
GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads
...esponsible for any damage resulting from the use of this software. The program package, including source cod...and this documentation, is distributed free of charge. If you use this program in a publication, please cite...2196 days ago
SOAP2 : Short Oligonucleotide Analysis Package 2
...mber of the SOAP (Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast and ac...2187 days ago