Software Updates

Qt

a cross-platform application framework that is used for developing application software that can be run on various software and hardware platforms with little or no change in the underlying codebase, while still being a native application with native capabilities and speed.

Quartz

(QUAlity score Reduction at Terabyte scale) an efficient de novo quality score compression tool based on traversing the k-mer landscape of NGS read datasets.

CORA

(COmpressive Read-mapping Accelerator) a compressive-acceleration tool for NGS read mapping methods.

DIAMOND

a high-throughput program for aligning a file of short DNA sequencing reads against a protein reference database such as NR, at 20,000 times the speed of BLASTX, with high sensitivity.

Quartz

(QUAlity score Reduction at Terabyte scale) an efficient de novo quality score compression tool based on traversing the k-mer landscape of NGS read datasets.

CORA

(COmpressive Read-mapping Accelerator) a compressive-acceleration tool for NGS read mapping methods.

MrBayes

a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.

BLAT

(BLAST-Like Alignment Tool) a very fast sequence alignment tool similar to BLAST.

DIAMOND

a high-throughput program for aligning a file of short DNA sequencing reads against a protein reference database such as NR, at 20,000 times the speed of BLASTX, with high sensitivity.

OpenJDK

(Open Java Development Kit) is a free and open source implementation of the Java Platform, Standard Edition (Java SE).

MICA

(Metagenomic Inquiry Compressive Acceleration) a family of programs for performing compressively-accelerated metagenomic sequence searches based on BLASTX and DIAMOND.

Infernal

(INFERence of RNA ALignment) searches DNA sequence databases for RNA structure and sequence similarities and uses a special case of profile stochastic context-free grammars called covariance models (CMs). In many cases It is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.