(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.
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.
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.
(Open Java Development Kit) a free and open source implementation of the Java Platform, Standard Edition (Java SE).
(Metagenomic Inquiry Compressive Acceleration) a family of programs for performing compressively-accelerated metagenomic sequence searches based on BLASTX and DIAMOND.
(INFERence of RNA ALignment) a program that 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.
