From the Caffe website: Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by Berkeley AI Research ( BAIR ) and by community contributors. Yangqing Jia created the project during his PhD at UC Berkeley. Caffe is released under the BSD 2-Clause license .
ABySS is a de novo, parallel, paired-end genomic sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes. To assemble transcriptome data, consider the related program trans-abyss. Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss
From the Pilon documentation: "Pilon uses read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies as well as call variants."
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 (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.