Software updates and installs since May 1st:
NOTE: All software is installed under the Lmod module system on Odyssey. And please read our guidelines for software install requests.
| armadillo | 5.100.2 | Fast C++ matrix library with easy to use functions and syntax, deliberately similar to Matlab |
| ART | 031915 | Simulation tools to generate synthetic next-generation sequencing reads |
| bcftools | 1.2 | Set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF |
| BEAST | 1.8.2 | Bayesian Evolutionary Analysis by Sampling Trees |
| BEAST | 2.1.3 | Bayesian Evolutionary Analysis by Sampling Trees |
| bismark | 0.14.2 | Bisulfate read mapper and methylation caller |
| clustalo | 1.2.0 | Multiple sequence alignment |
| cutadapt | 1.8.1 | Trims adapter sequence from fastq files |
| emboss | 6.6.0 | EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community |
| FragGeneScan | 1.19 | Application for finding (fragmented) genes in short reads. |
| GenomeAnalysisTK | 3.3.0 | Genome Analysis ToolKit version 3.3.0 |
| libmesh | 0.9.4 | Framework for numerical simulation of partial differential equations |
| MaxBin | 1.4.5 | An automatic tool for binning metagenomics sequences |
| netcdf | 4.3.2 | Libraries for array-oriented scientific data format |
| oommf | 1.2a5bis | Object Oriented MicroMagnetic Framework |
| OpenBLAS | 0.2.14 | Open source linear algebra library |
| petsc | 3.5.4 | Portable extensible toolkit for scientific computation |
| samtools | 1.2 | Utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. |
| slepc | 3.5.4 | Scalable library for eigenvalue problem computations |
| SPAdes | 3.5.0 | St. Petersburg genome assembler for both standard isolates and single cell MDA bacteria |
| SweeD | 3.3.2 | Composite likelihood ratio test for detecting selective sweeps |
| tcl | 8.6.4 | Dynamic programming language, suitable for a very wide range of uses |
| tk | 8.6.4 | Open source, cross-platforM widget toolkit |
| trinityrnaseq | 2.0.6 | De novo assembler from RNA Seq from Broad Inst. et al. |
| trinityrnaseq | r20140717 | De novo assembler from RNA Seq from Broad Inst. et al. |
| vapor | 2.4.0 | Visualization and Analysis Platform for Ocean, Atmosphere, and Solar Researchers |
| VarScan | 2.3.7 | Variant detection in massively parallel sequencing data |
| visit | 2.9.1 | Open Source, interactive, scalable, visualization, animation and analysis tool |
Last updated: December 5, 2017 at 14:02 pm