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