A-E

ABINIT:

ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and

nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.

Versions:

ABINIT/9.4.2-foss-2021a

ABINIT/9.6.2-intel-2021b

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ABySS: ABySS/2.2.5-foss-2020b

Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

More information

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- Homepage: https://www.bcgsc.ca/platform/bioinfo/software/abyss

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ASE: ASE/3.20.1-fosscuda-2020b

ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language. From version 3.20.1 we also include the

ase-ext package, it contains optional reimplementations in C of functions in ASE. ASE uses it automatically when installed.

From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations

in C of functions in ASE. ASE uses it automatically when installed.

More information

================

- Homepage: https://wiki.fysik.dtu.dk/ase

Included extensions

===================

ase-3.20.1, ase-ext-20.9.0

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AUGUSTUS: AUGUSTUS/3.4.0-foss-2021b

AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences

More information

================

- Homepage: https://bioinf.uni-greifswald.de/augustus/

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AlphaFold: AlphaFold/2.1.2-foss-2021a-CUDA-11.3.1

AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known.

More information

================

- Homepage: https://deepmind.com/research/case-studies/alphafold

Included extensions

===================

chex-0.0.8, contextlib2-21.6.0, dm-haiku-0.0.4, dm-tree-0.1.6, docker-5.0.0,

immutabledict-2.1.0, ml_collections-0.1.0, PDBFixer-1.7, tabulate-0.8.9,

toolz-0.11.1, websocket-client-1.2.1

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Amber: Amber/20.11-fosscuda-2020b-AmberTools-21.3

Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction.

More information

================

- Homepage: http://ambermd.org/amber.html

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Arrow:

Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform for in-memory data.

Versions:

Arrow/6.0.0-foss-2021b

Arrow/8.0.0-foss-2021a

Arrow/8.0.0-foss-2022a

Other possible modules matches:

arrow-R

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BBMap: BBMap/38.98-GCC-11.2.0

BBMap short read aligner, and other bioinformatic tools.

More information

================

- Homepage: https://sourceforge.net/projects/bbmap/

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BCFtools:

Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and

calling/filtering/summarising SNP and short indel sequence variants

Versions:

BCFtools/1.12-GCC-10.3.0

BCFtools/1.14-GCC-11.2.0

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BEDTools:

BEDTools: a powerful toolset for genome arithmetic. The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps

and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.

Versions:

BEDTools/2.30.0-GCC-11.2.0

BEDTools/2.30.0-iccifort-2020.4.304

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BLAST+: BLAST+/2.12.0-gompi-2021b

Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of

different proteins or the nucleotides of DNA sequences.

More information

================

- Homepage: https://blast.ncbi.nlm.nih.gov/

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BUSCO: BUSCO/5.4.3-foss-2021b

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

More information

================

- Homepage: https://busco.ezlab.org/

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BWA:

Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the

human genome.

Versions:

BWA/0.7.17-GCC-10.3.0

BWA/0.7.17-GCCcore-11.2.0

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BamTools:

BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.

Versions:

BamTools/2.5.1-iccifort-2020.4.304

BamTools/2.5.2-GCC-11.2.0

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Biopython:

Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed

collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.

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Bison:

Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser

employing LALR(1) parser tables.

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Boost:

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

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Bowtie2: Bowtie2/2.4.4-GCC-11.2.0

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads

of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the

genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports

gapped, local, and paired-end alignment modes.

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CUDA:

CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the

graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational

elements in CUDA GPUs.

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CellRanger: CellRanger/6.1.2

Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate gene-cell matrices and perform

clustering and gene expression analysis.

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Cufflinks:

Transcript assembly, differential expression, and differential regulation for RNA-Seq

More information

================

- Homepage: http://cole-trapnell-lab.github.io/cufflinks/

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DendroPy:

A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees

(phylogenies) and characters.

More information

================

- Homepage: https://dendropy.org/

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EMBOSS:

EMBOSS is 'The European Molecular Biology Open Software Suite' . EMBOSS is a free Open Source software analysis package specially developed for the

needs of the molecular biology (e.g. EMBnet) user community.

More information

================

- Homepage: http://emboss.sourceforge.net/

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Eigen:

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