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Software

software::software.applied filters:

Abacas is a tool for algorithm based automatic contiguation of assembled sequences.

Available Versions
Available Versions
Unspecified: 1.3.1

Abaqus is a software suite for Finite Element Analysis (FEA) developed by Dassault Systèmes.

Available Versions
Available Versions
Bell: 2019 2020 2021 2022 2023
Gilbreth: 2017 2018 2019 2020 2021 2022
Negishi: 2022
Scholar: 2017 2018 2019 2020 2021 2022 6.14-6

adaptive banded Partial Order Alignment

Available Versions
Available Versions
Unspecified: 1.4.1

Abricate is a tool for mass screening of contigs for antimicrobial resistance or virulence genes.

Available Versions
Available Versions
Unspecified: 1.0.1

ABySS is a de novo sequence assembler intended for short paired-end reads and genomes of all sizes.

Available Versions
Available Versions
Unspecified: 2.3.2 2.3.4

Actc is used to align subreads to ccs reads.

Available Versions
Available Versions
Unspecified: 0.2.0

AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.

Available Versions
Available Versions
Unspecified: 2.3.3

Advntr is a tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data.

Available Versions
Available Versions
Unspecified: 1.4.0 1.5.0

Afplot is a tool to plot allele frequencies in VCF files.

Available Versions
Available Versions
Unspecified: 0.2.1

Afterqc is a tool for quality control of FASTQ data produced by HiSeq 2000/2500/3000/4000, Nextseq 500/550, MiniSeq, and Illumina 1.8 or newer.

Available Versions
Available Versions
Unspecified: 0.9.7

Agat is a suite of tools to handle gene annotations in any GTF/GFF format.

Available Versions
Available Versions
Unspecified: 0.8.1

AGFusion (pronounced 'A G Fusion') is a python package for annotating gene fusions from the human or mouse genomes.

Available Versions
Available Versions
Unspecified: 1.3.11

Alfred is an efficient and versatile command-line application that computes multi-sample quality control metrics in a read-group aware manner.

Available Versions
Available Versions
Unspecified: 0.2.5 0.2.6

Alien-hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs).

Available Versions
Available Versions
Unspecified: 1.7.7

AlignStats produces various alignment, whole genome coverage, and capture coverage metrics for sequence alignment files in SAM, BAM, and CRAM format.

Available Versions
Available Versions
Unspecified: 0.9.1

Allpathslg is a whole-genome shotgun assembler that can generate high-quality genome assemblies using short reads.

Available Versions
Available Versions
Unspecified: 52488

Alphafold is a protein structure prediction tool developed by DeepMind (Google). It uses a novel machine learning approach to predict 3D protein structures from primary sequences alone.

Available Versions
Available Versions
Unspecified: 2.1.1 2.2.0 2.2.3 2.3.0 2.3.1

AMBER (Assisted Model Building with Energy Refinement) is a package of molecular simulation programs.

Available Versions
Available Versions
Anvil: 20
Bell: 16
Gilbreth: 16
Negishi: 20
Scholar: 16

AMD LibM is a software library containing a collection of basic math functions optimized for x86-64 processor-based machines. It provides many routines from the list of standard C99 math functions. Applications can link into AMD LibM library and invoke math functions instead of compilers math functions for better accuracy and performance.

Available Versions
Available Versions
Anvil: 3.0

AMD Optimized BLIS. BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.

Available Versions
Available Versions
Anvil: 3.0