HPC/Linux

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.

RECON

RECON is software for automated de novo identification of repeat families from genomic sequences.

 

This software was originally developed by the Eddy lab. A newer version that fixes several bugs is available from the RepeatMasker webpage.

GNU Scientific Library

From the GNU website:

"The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License.

The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite."

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