Available Software on Altamira Supercomputer

Updated: 2012-03-12

Compilers, Interpreters and Development Utils

gcc /4.6.3 (also 4.7.2 y 3.4.6 )

Gnu C++, Fortran

INTEL /PSXE2013u1

INTEL Parallel Studio XE2013: C++, Fortran

JAVA /1.6u33

(also jdk)

PERL /5.16.1

PYTHON /2.7.3

CMAKE /2.8.7

Utilidad make

LLVM /3.1

Open Source C/C++ (incl. clang)

DDD /3.3.12

Data Display Debugger (interfaz a debugger)

HASKELL PLATFORM /2012.2.0.0

Glasgow Haskell Compiler + Basic Haskell Libs

ANT /1.8.4

Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other.

Development Libraries

OPENMPI

Open source MPI-2 implementation that is developed and maintained by a consortium of academic, research, and industry

MVAPICH2

MPI-3 over OpenFabrics-IB, OpenFabrics-iWARP, PSM, uDAPL and TCP/IP

GSL /1.15

GNU Scientific Library (GSL) is a numerical library for C and C++ programmers

BOOST /1.52.0

Boost provides free peer-reviewed portable C++ source libraries

BEAGLE /r1090

A high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. It can make use of highly-parallel processors such as those in graphics cards (GPUs)

NETCDF /4.2.1.1

NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

HDF5 /1.8.10

HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data

GDAL /1.9.2

is a translator library for raster geospatial data formats

PROJ4 /4.8.0

Cartographic Projections library

CUDA /4.2.9

a parallel computing platform and programming model to exploit the power of graphics processing unit (GPU)

LUAJIT /2.0

a Just-In-Time Compiler for Lua.

PAPI /5.0.1

The Performance API (PAPI) project specifies a standard application programming interface (API) for accessing hardware performance counters available on most modern microprocessors.

Applications

General

MATLAB /R2010b

Lenguaje de alto nivel y un entorno interactivo para el cálculo numérico, la visualización y la programación. VERSION EN PARALELO.

SAGE /5.3

Open source alternative to MATLAB

R /2.15.1

Free software environment for statistical computing and graphics. VERSION EN PARALELO

High Energy & Nuclear Physics

ROOT /5.34.01

An object oriented framework for large scale data analysis developed at CERN. VERSION EN PARALELO: PROOF

CMS SW

Software setup for the CMS collaboration at CERN

Quantum Models for Atoms and Molecules

SIESTA /3.1

A method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.

CPMD /3.15.1

Car-Parrinello Molecular Dynamics: An ab initio Electronic Structure and Molecular Dynamics Program

DL_POLY /2.20

a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory

LAMMPS /22Feb13

a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

VASP /5.3_INTEL

The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.

Computing Science

EXTRAE /2.3

is a dynamic instrumentation package to trace programs compiled and run with the shared memory model (like OpenMP and pthreads), the message passing (MPI) programming model or both programming models (different MPI processes using OpenMP or pthrads within each MPI process)

Bio

MPIBLAST /1.6.0

open-source, parallel implementation of NCBI BLAST. BLAST finds regions of similarity between biological sequences.

GPU-BLAST /1.1

an accelerated GPU version of the popular NCBI-BLAST.

BLAT /35

The BLAST-Like Alignment Tool

MrBayes /3.2.1

a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models

BEAST /1.7.5

cross-platform program for Bayesian MCMC analysis of molecular sequences. Uses BEAGLE.

MIRA /3.4.0.1

whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads).

BEDTOOLS /2.17.0

allow one to address common genomics tasks such as finding feature overlaps and computing coverage.

BEST /2.3.1

a phylogenetics program to estimate the joint posterior distribution of gene trees and species tree using multilocus molecular data that accounts for deep coalescence but not for other issues such as horizontal transfer or gene duplication

BIOPERL /1.6.1

a community effort to produce Perl code which is useful in biology.

PAML /4.6

package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.

PARTITIONFINDER /1.0.1

Free open source programs for selecting best-fit partitioning schemes and models of molecular evolution for nucleotide and amino acid alignments.

PICARD_TOOLS /1.79

Java-based command-line utilities that manipulate SAM (Sequence Alignment/Map) files, and a Java API (SAM-JDK) for creating new programs that r&w SAM files

PINDEL /0.2.4d

detects breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data.

BOWTIE /2.0.2

an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour.

PROTTEST /3.2

bioinformatic tool for the selection of best-fit models of aminoacid replacement for the data at hand.

PhyML /20120412

estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences

BWA /0.6.2

for aligning sequencing reads against a large reference genome (e.g. human genome).

PhyloBayes /3.3e

is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction

RAxML /7.3.1

implements the popular RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. It uses a radically new MPI parallelization approach that yields improved parallel efficiency, in particular on partitioned multi-gene or whole-genome datasets.

FASTQC /0.10.1

A quality control tool for high throughput sequence data.

SAMTOOLS /0.1.18

provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

GATK /2.2-8

The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data.

SOAPdenovo /1.05

novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads.

HMMER /3.0 (also 2.3.2-MPI-0.92, GPU-0.92)

is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs)

TOPHAT /2.0.6

is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie and then analyzes the mapping results to identify splice junctions between exons.

TRINITY_RNA_SEQ /r2012-06-08

implements a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.

INTERPROSCAN /5-RC4

allows you to scan your sequence for matches against the InterPro collection of protein signature databases

JMODELTEST /2.1.1

a tool to carry out statistical selection of best-fit models of nucleotide substitution