Versions Compared

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Name

Versions (Min - Max)

Description

Abseil

20230125.2

Google’s C++ library providing foundational components for modern C++ code.

Armadillo

11.4.3-foss-2022b

C++ linear algebra library with MATLAB-like syntax.

Arpack-ng

3.8.0-foss-2022b

A library for solving large-scale eigenvalue problems (sparse matrices).

ATK

2.38.0 ,2.46.0

 Framework for creating accessible applications in GNOME.

Autoconf

2.71 - 2.72

Tool for generating automatic configuration scripts in software projects.

Autotools

1.16.5 - 1.16.5

Suite of tools (Autoconf, Automake, Libtool) for compiling and packaging software.

Binutils  

2.38 - 2.42

Collection of binary tools (e.g., ld, as, objdump) for handling object files.

Bison

3.8.2   

Parser generator (YACC replacement) for converting grammar rules into code.

BLIS

0.9.0

High-performance BLAS (Basic Linear Algebra Subprograms) library.

Boost

1.81-1.82

Extensive C++ library collection for tasks like multithreading, algorithms, and data structures.

Brotli

1.0.9

Google’s compression algorithm/library for efficient data compression.

Brunsli

0.1

Lossless JPEG repacking library (improves compression).

bzip2

1.0.8

Compression library and tool for lossless data compression.

cairo

1.17.4, 1.17.8, 12.3.0 , 1.18.0

2D graphics library supporting vector and raster output (used in GTK, browsers).

CASTEP

25.1.1-intel-2024a, 25.1.1-foss-2023b

First-principles quantum mechanics code for materials modeling.

Catch2

2.13.9

Modern C++ testing framework (header-only, simple syntax).

cffi

1.15.1

Foreign function interface (FFI) for Python to call C code.

CFITSIO

4.2.0 - 4.3.1

Library for reading/writing FITS files (astronomy data format).

CGAL

5.6

Computational Geometry Algorithms Library (C++ templates for geometric operations).

CMake 

3.24.3 -  3.29.3

Cross-platform build system generator (replaces Makefiles).

crytography

41.0.1, 41.0.5

Python library for secure cryptographic operations (e.g., encryption, hashing).

cURL

7.86.0 - 8.7.1

Command-line tool and library for transferring data with URLs (supports HTTP, FTP, etc.).

Cython

3.0.10

Python-to-C compiler for writing C extensions in Python-like syntax.

DB

18.1.40

Embedded database library for key-value storage.

DBus

1.15.2 - 1.15.4

Message bus system for inter-process communication (IPC) in Linux.

double-conversion

3.3.0

Library for precise binary-decimal number conversion (used in V8, LLVM).

Doxygen

1.9.5 - 1.11.0

Documentation generator for C++, C, Java, etc. (extracts comments into docs).

Easybuild

4.9.1, 5.0.0

Framework for automating software builds on HPC systems.

Eigen

3.4.0

C++ template library for linear algebra (matrices, vectors, numerical solvers).

expat

2.4.8 - 2.6.2

Stream-oriented XML parser library written in C.

FFmpg

6.0

Multimedia framework for handling audio/video (encoding, decoding, streaming).

ffnvcodec

12.0.16.0

NVIDIA’s hardware-accelerated video codec SDK (for FFmpeg).

FFTW

3.3.10

Fastest Fourier Transform in the West (C library for FFT computations).

FLAC

1.4.2

Free Lossless Audio Codec for compressed audio without quality loss.

flex

2.6.4

Fast lexical analyzer generator (lexical tokenizer, often used with Bison).

FlexiBLAS

3.2.1 - 3.4.4

A flexible BLAS (Basic Linear Algebra Subprograms) wrapper that allows runtime switching between different BLAS implementations.

flit

3.9.0

A simple Python packaging tool for pure-Python modules (alternative to setuptools).

fontconfig

2.14.1 - 2.15.0

A library for configuring and customizing font access in Linux/Unix systems (used by GUI apps).

fonttools

4.53.1

A Python library for manipulating fonts (e.g., OpenType, TrueType) programmatically.

foss

2022b -  2024a

Free and Open Source Software tools

freeglut

3.4.0

 An open-source alternative to GLUT (OpenGL Utility Toolkit) for creating OpenGL windows and handling input.

freetype

2.12.1

A widely used library for rendering fonts (supports multiple font formats like TTF, OTF).

friBidi

1.0.12 ,1.0.15

A library for handling bidirectional text (e.g., Arabic, Hebrew mixed with left-to-right languages).

GCC

12.2.0 - 13.2.0

A suite of compilers for C, C++, Fortran, Ada, and other languages.

GCCcore

11.3.0 - 13.3.0

Core GNU Compiler Collection (C/C++/Fortran compilers) without OS dependencies

GDAL

3.6.2-foss-2022b 

Geospatial Data Abstraction Library for raster/vector geospatial formats

Gdk-Pixbuf

2.42.10

Image loading/manipulation library for GTK+ GUI toolkit

GEOS

3.11.1

Geometry Engine - Open Source (computational geometry library)

gettext

0.21.1,0.22.5

GNU internationalization/i18n framework for multi-language software

gfbf

2022b - 2024a

EasyBuild toolchain (GCC + FFTW + BLAS/LAPACK + ScaLAPACK)

Ghostscript

10.0.0

PostScript/PDF interpreter and rendering engine

giflib

5.2.1

Library for reading/writing GIF image format

git

2.38.1 - 2.45.1

Distributed version control system

GL2PS

1.4.2

OpenGL to PostScript/PDF/SVG exporter

GLib

2.75.0 - 2.80.4

Core application building blocks for GNOME (data structures, I/O, threading)

GLPK

5.0

GNU Linear Programming Kit (solver for optimization problems)

GMP

6.2.1

GNU Multiple Precision Arithmetic Library

gnuplot

5.4.8

Command-line driven graphing/plotting utility

GObject-Introspection

1.74.0 - 1.90.1

Middleware for language bindings to C libraries

gompi

2022b - 2024a

EasyBuild toolchain (GCC + OpenMPI)

googletest

1.12.1

Google's C++ testing framework

gperf

3.1

Perfect hash function generator

graphite2

1.3.14

Smart font rendering engine for complex scripts

groff

1.22.4 - 1.23.0

GNU troff document formatting system (man pages)

GSL

2.7

GNU Scientific Library (numerical algorithms)

GTK3

3.24.35

GIMP Toolkit v3 (GUI widget toolkit)

gzip

1.12,1.13

File compression/decompression utility

HarfBuzz

5.3.1, 9.0.0

Text shaping engine (OpenType font rendering)

hatchling

1.18.0

Modern Python build backend/packaging tool

HDF

4.2.15

Hierarchical Data Format (legacy version)

HDF5

1.12.2 - 1.14.3

Hierarchical Data Format v5 (data management for large datasets)

help2man

1.49.2,1.49.3

Automated man page generator from --help output

hwloc

2.8.0 - 2.10.0

Portable Hardware Locality (hardware topology mapping)

hypothesis

6.68.2 - 6.90.0

Property-based testing framework for Python

ICU

72.1 - 75.1

International Components for Unicode (i18n/l10n)

iimpi

2022a - 2024a

EasyBuild toolchain (Intel compilers + Intel MPI)

ImageMagick

7.1.0-53

Image manipulation/conversion CLI suite

Imath

3.1.6

Math library for computer graphics (originally from ILM)

imkl-FFTW

2022.1.0 - 2024.2.0

Intel Math Kernel Library's FFTW3-compatible interface

imkl

2022.1.0 - 2024.2.0

Intel Math Kernel Library (optimized math routines)

impi

2021.6.0 - 2021.13.0

Intel C/C++/Fortran compilers (icc/icpc/ifort)

intel-compilers

2022.1.0 - 2024.2.0

Meta-module for Intel development tools

INTEL

2023.0, 2024.0


intltool

0.51.0

Internationalization toolkit for source code

JasPer

4.0.0

JPEG-2000 image codec implementation

Java

11.0.20, 17.0.6

Oracle Java Development Kit/Runtime

jbigkit

2.1

JBIG1 image compression library

jq

1.6

Lightweight JSON processor (CLI tool)

 json-c

0.16

JSON library for C applications

 KaHIP

3.16

Karlsruhe High Quality Partitioning (graph partitioning)

 LAME

3.100

MP3 audio encoder

 LERC

4.0.0

Limited Error Raster Compression (geospatial)

 libarchive

3.6.1 - 3.7.4

Multi-format archive/library compression

 libcerf

2.3

Complex error function library

 libdeflate

1.15, 1.20

Fast DEFLATE/zlib/gzip compression

 libdrm

2.4.114 - 2.4.122

Direct Rendering Manager library (Linux graphics)

 libepoxy

1.5.10

GL dispatch library abstraction

libevent

2.1.12

Asynchronous event notification library

libfabric

1.16.1 - 1.21.0

OpenFabrics Interfaces (high-performance networking)

libff

3.4.4, 3.4.5

Foreign Function Interface library (calling between languages)

libgd

2.3.3

Graphics drawing library (dynamic image creation)

libgeotiff

1.7.1

GeoTIFF GIS metadata handling library

libgit2

1.5.0, 1.8.1

Portable Git implementation library

libGLU

9.0.2, 9.0.3

OpenGL Utility Library (higher-level graphics helpers)

libglvnd

1.6.0, 1.7.0

Vendor-neutral GL dispatch library

libiconv

1.17

Character encoding conversion library

libjpeg-turbo

2.1.4, 2.1.5, 3.0.1

Accelerated JPEG codec with SIMD support

libogg

1.3.5

Ogg multimedia container library

libopus

1.3.1

Opus audio codec implementation

libpciaccess

0.17, 0.18

Uniform interface to PCI devices

libpng

1.6.38 - 1.6.43

Reference implementation for PNG image format handling

libreadline

8.1.2, 8.2

Interactive command-line editing library (used in bash, Python, etc.)

libsndfile

1.2.0

Audio file I/O library supporting WAV, AIFF, FLAC, OGG, and others

LibTIFF

4.4.0, 4.6.0

Library for reading/writing TIFF image format with metadata support

libtirpc

1.3.3

Transport-independent RPC implementation (SunRPC replacement)

libtool

2.4.7

Generic library support script for building shared libraries portably

libunwind

1.6.2, 1.8.1

Stack unwinding library for exception handling and debugging

libvorbis

1.3.7

Reference implementation of Vorbis audio compression format

libxml2

2.10.3 - 2.12.7

XML parsing library with DOM, SAX, and XPath support

libxslt

1.1.37

XSLT processing library based on libxml2

lit

18.1.8

LLVM Integrated Tester (lightweight testing tool)

LittleCMS

2.14

Color management engine (ICC profile handling)

LLVM

15.0.5 - 18.1.8

Compiler infrastructure project (clang, lldb, opt, etc.)

Lua

5.4.6

Lightweight embeddable scripting language

lz4

1.9.4

Extremely fast lossless compression algorithm

M4

1.4.19

Macro processor (preprocessor for configure scripts)

make

4.3 - 4.4.1

Build automation tool that executes Makefiles

Mako

1.2.4 - 1.3.5

Python templating library (similar to Jinja2)

MATLAB

2025a

Numerical computing environment and proprietary language

Mesa

22.2.4 - 24.1.3

Open-source OpenGL/Vulkan implementation (3D graphics)

meson-python

0.15.0

Python build backend using Meson build system

Meson

0.64.0 - 1.4.0

Modern build system focusing on speed and simplicity

METIS

5.1.0

Graph partitioning and fill-reducing matrix ordering library

MPFR

4.2.0

Multiple-precision floating-point computations library

NASM

2.15.05 - 2.16.03

Netwide Assembler for x86/x64 architectures

ncurses

6.3 - 6.5

Terminal UI library for text-based interfaces

netCDF-Fortran

4.6.0, 4.6.1

Fortran interface to netCDF data format

netCDF

4.9.0, 4.9.2

Network Common Data Format for scientific array data

nettle

3.8.1

Low-level cryptographic library

Ninja

1.11.1

Small build system focused on speed

nlohmann_json

3.11.2

C++ header-only JSON parser/serializer

NLopt

2.7.1

Nonlinear optimization library with C/C++ interfaces

nodejs

18.12.1, 18.17.1

JavaScript runtime built on Chrome's V8 engine

NSPR

4.35

Netscape Portable Runtime (platform abstraction layer)

NSS

3.89.1

Network Security Services (crypto library for browsers)

numactl

2.0.14 - 2.0.18

NUMA (Non-Uniform Memory Access) control utilities

OpenBLAS

0.3.21 - 0.3.27

Optimized BLAS/LAPACK implementation with multi-threading

OpenEXR

3.1.5

High dynamic-range (HDR) image file format by ILM

OpenFOAM

v2312-foss-2023a

Open-source computational fluid dynamics (CFD) toolkit

OpenJPEG

2.5.0

JPEG 2000 codec implementation

OpenMPI

4.1.4 - 5.0.3

High-performance MPI (Message Passing Interface) implementation

OpenSSL

1.1, 3

Cryptography/TLS toolkit implementing SSL protocols

Pango

1.50.12, 1.50.14

Text layout/rendering library for internationalization

ParaView

5.11.2-foss-2023a

 Scientific visualization application for large datasets

patchelf

0.18.0

Modify ELF binaries (RPATH, interpreter)

PCRE

8.45

Perl Compatible Regular Expressions library

PCRE2

10.40 - 10.43

Modern successor to PCRE with improved Unicode support

Perl-bundle-CPAN

5.36.1, 5.38.2

Comprehensive Perl Archive Network modules collection

Perl

5.34.1 - 5.38.2

Practical Extraction and Reporting Language

pixman

0.42.2, 0.43.4

Low-level pixel manipulation library

pkgconf

1.8.0 - 2.2.0

System to manage compile/link flags (pkg-config replacement)

PMIx

4.2.2 - 5.0.2

Process Management Interface for Exascale environments

poetry

1.5.1, 1.6.1

Python dependency management and packaging tool

PROJ

9.1.1

Coordinate transformation library for geospatial data

protobuf

23.0

Protocol Buffers data serialization format (Google)

PRRTE

3.0.5

Reference RunTime Environment for PMIx

pybind11

2.10.3, 2.11.1

Seamless interoperability between C++ and Python

Python-bundle-PyPI

2023.06, 2023.10

Collection of Python packages from PyPI

Python

3.10.8 - 3.12.3

High-level interpreted programming language

Qhull

2020.2

Convex hull, Delaunay triangulation library

Qt5

5.15.10

Cross-platform application framework for GUIs

R

4.2.2-foss-2022b, 4.4.2

Statistical computing and graphics language

re2c

3.1

Lexer generator for C/C++

ROOT

6.26.10, 6.30.06

Data analysis framework (CERN particle physics)

Rust

1.65.0 - 1.73.0

Systems programming language focused on safety

ScaLAPACK

2.2.0

Scalable Linear Algebra PACKage for parallel systems

scikit-build

0.17.6

Improved build system generator for Python

SciPy-bundle

2023.02 - 2023.11

 Collection of Python scientific libraries

SCOTCH

7.0.3

Graph partitioning and mesh handling library

SDL2

2.28.2

Simple DirectMedia Layer (cross-platform multimedia)

setuptools-rust

1.6.0, 1.8.0

Rust support for Python setuptools

snappy

1.1.10

Fast compression/decompression library by Google

SQLite

3.39.4 - 3.45.3

Embedded relational database engine

Szip

2.1.1

Lossless data compressor for scientific data

Tcl

8.6.12 - 8.6.14

Tool Command Language scripting language

tcsh

6.24.07

C shell with command-line completion

time

1.9

Command execution timing utility

Tk

8.6.12 - 8.6.14

GUI toolkit for Tcl

UCC

1.1.0 * 1.3.0

Unified Collective Communication Library

UCX

1.12.1 - 1.16.1

Unified Communication X framework for HPC

UDUNITS

2.2.28

Unit conversion library for physical quantities

UnZip

6.0

Extraction utility for ZIP archives

util-linux

2.38.1 - 2.40.0

Collection of Linux system utilities

virtualenv

20.23.1, 20.24.6

Python environment isolation tool

Wayland

1.23.0

Display server protocol (modern X11 replacement)

WRF

4.4.1

Weather Research and Forecasting model

X11

20221110, 20230603, 20240607

Core protocol for X Window System

x264

20230226

H.264/AVC video encoder

x265

3.5

H.265/HEVC video encoder

Xerces-C++

3.2.4

XML parser and toolkit for C++

xorg-macros

1.19.3 - 1.20.1

GNU autoconf macros for X.Org development

Xvfb

21.1.6

X server in virtual framebuffer memory

XZ

5.2.7 - 5.4.5

Lossless data compression with LZMA algorithm

Yasm

1.3.0

Modular assembler for x86 optimization

zlib

1.2.12, 1.2.13, 1.3.1

Compression library (DEFLATE algorithm)

zstd

1.5.2 - 1.5.6

Fast real-time compression algorithm

Development Libraries

...

Name

...

Version: Default(Others)

...

Description

...

ARGTABLE

...

2.13

...

ANSI C library for parsing GNU style command line options with a minimum of fuss

...

ASTRON

...

2014

...

IDL Astronomy Users Library

...

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)

...

BOOST

...

1.52.0

...

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

...

CANTERA

...

2.2.0(also 2.2.1)

...

Open-source collection of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and transport processes

...

CGIS

...

4.1

...

CLASS

...

Nov2011

...

CUDA

...

4.2.9(also 4.0.17, 7.0.28, 7.5.18)

...

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

...

EIGEN

...

3.8.2

...

C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.

...

GDAL

...

1.9.2

...

is a translator library for raster geospatial data formats

...

GSL

...

1.15 (1.15 (also 1.15INTEL, 1.5_ICC, 2.3)

...

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

...

HDF5

...

1.8.10 (also 1.8.10INTEL, 1.8.16, 1.8.8_ICC)

...

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

...

IGRAPH

...

0.7.1

...

Collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++

...

LAPACK

...

3.4.1

...

Linear Algebra PACKage

...

LIBTOOL

...

2.4.2

...

Generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.

...

LUAJIT

...

2.0

...

A Just-In-Time Compiler for Lua.

...

MPFIT

...

1.3

...

A MINPACK-1 Least Squares Fitting Library in C

...

MPICH

...

3.0.4 (also 3.0.4_ICC)

...

A high performance and widely portable implementation of MPI standard.

...

MVAPICH2

...

2.0 (also 2.1rc1, 2.2)

...

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

...

NETCDF

...

4.2.1.1 (also 4.1.3, 4.4.0 and fortran 4.4.3)

...

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.

...

OPENBLAS

...

0.2.15

...

Optimized BLAS library based on GotoBLAS2 1.13 BSD version

...

OPENMPI

...

1.8.3(also 4.0.1, 1.8.4rc1, 1.8.3_ICC,1.6.5,1.6.3_ICC,1.4.5)

...

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

...

PAPI

...

5.4.0(also 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.

...

PROJ4

...

4.8.0

...

Cartographic Projections library

...

QT4

...

4.8.5

...

Cross-platform application development framework for desktop, embedded and mobile

Applications

General

...

Name

...

Version: Default (Others)

...

Description

...

ANSYS

...

2019R3

...

CFD simulation package for internal combustion engines

...

MATLAB

...

R2019b

...

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

...

SAGE

...

5.3 (also 6.4.1)

...

Open source alternative to MATLAB

...

R

...

2.15.1 (also 3.2.3, 3.2.1)

...

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

High Energy & Nuclear Physics

...

Name

...

Version: Default (Others)

...

Description

...

ROOT

...

5.34.01 (also 5.34.17)

...

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

...

Name

...

Version: Default (Others)

...

Description

...

SIESTA

...

3.1 (also 4.0)

...

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

...

5.4.4_INTEL

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

...

Name

...

Version: Default (Others)

...

Description

...

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 pthreads within each MPI process)

Bio

...

Name

...

Version: Default (Others)

...

Description

...

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.

...

NETLOGO

...

5.3(also 5.2.1)

...

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.

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PROTTEST

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3.2

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

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PhyML

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20120412

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

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BWA

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0.6.2

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

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PhyloBayes

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3.3e

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

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RAxML

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7.3.1

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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.

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FASTQC

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0.10.1

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A quality control tool for high throughput sequence data.

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SAMTOOLS

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0.1.18 (also 1.3 and 1.5)

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

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GATK

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2.2-8

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

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SOAPdenovo

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1.05

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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.

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HMMER

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

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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)

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TOPHAT

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2.0.6

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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.

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TRINITY_RNA_SEQ

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r2012-06-08

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

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INTERPROSCAN

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5-RC4

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

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JMODELTEST

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2.1.1

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