HPC/Linux

Qiime2

QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results. QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis pipeline.

RAxML

RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It can also be used for post- analyses of sets of phylogenetic trees, analyses of alignments and, evolutionary placement of short reads.

 

 

OrthoFinder

From the OrthoFinder website:

Accurate inference of orthologous gene groups made easy. "OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthologous gene group inference accuracy"

Caffe

From the Caffe website:

FALCON

FALCON and FALCON-Unzip provide algorithms to assemble Single Molecule Real-Time (SMRT(R)) Sequencing data into highly accurate, contiguous, and correctly phased diploid genomes. 

UnRar

UnRar is a utility for extracting WinRar archives (.rar files).

HISAT2

From the HISAT webpage:

NCCL

From the NCCL website:

STAR

Spliced Transcripts Alignment to a Reference (STAR) is a software package developed for aligning large RNA-seq datasets.

CP2K

From cp2k.org:

CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems.

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