genewise: a program for aligning proteins or protein HMMs to DNA, and dynamite a rather cranky "macro language" which automates the production of dynamic programming.
最近更新: 2年多前RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
最近更新: 2年多前LAMMPS is a classical molecular dynamics code with a focus on materials modeling. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain.
最近更新: 2年多前GraphMap is a novel mapper targeted at aligning long, error-prone third-generation sequencing data. It is designed to handle Oxford Nanopore MinION 1d and 2d reads with very high sensitivity and accuracy, and also presents a significant improvement over the state-of-the-art for PacBio read mappers.
最近更新: 2年多前The GATK, designed for human genome and exome analysis and extended to handle other organisms.
最近更新: 2年多前The Tinker molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. Tinker has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98, ff99, ff99SB), CHARMM (19, 22, 22/CMAP), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA), Merck Molecular Force Field (MMFF), Liam Dang's polarizable model, and the AMOEBA, AMOEBA+ and HIPPO polarizable atomic multipole force fields. Parameter sets for other widely-used force fields are under consideration for future releases.
最近更新: 2年多前FreeSurfer is a software package for the analysis and visualization of neuroimaging data from cross-sectional and longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Martinos Center for Biomedical Imaging.
最近更新: 2年多前AmberTools consists of several independently developed packages that work well by themselves, and with Amber22 itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.
最近更新: 2年多前CESM is a fully-coupled, community, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states.
最近更新: 2年多前GRIDSS is a multithreaded structural variant (SV) caller that performs efficient genome-wide break-end assembly prior to variant calling using a novel positional de Bruijn graph-based assembler. By combining assembly, split read, and read pair evidence using a probabilistic scoring, GRIDSS achieves high sensitivity and specificity on simulated, cell line, and patient tumor data, recently winning SV subchallenge #5 of the ICGC-TCGA DREAM8.5 Somatic Mutation Calling Challenge.
最近更新: 2年多前
