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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."


Bazel is a build tool from Google currently available in a public beta.


Phobius is "a combined transmembrane topology and signal peptide predictor". 


From the DIAMOND website:

"DIAMOND is a new high-throughput program for aligning DNA reads or protein sequences against a protein reference database such as NR, at up to 20,000 times the speed of BLAST, with high sensitivity."


From the MetAMOS website:

"MetAMOS represents a focused effort to create automated, reproducible, traceable assembly & analysis infused with current best practices and state-of-the-art methods. MetAMOS for input can start with next-generation sequencing reads or assemblies, and as output, produces: assembly reports, genomic scaffolds, open-reading frames, variant motifs, taxonomic or functional annotations, Krona charts and HTML report."


From the Pilon documentation:

"Pilon uses read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies as well as call variants."


LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a software suite for classical molecular dynamics simulations developed and maintained by Sandia National Labs.

NCO netCDF Operators

From the NCO website:

"The netCDF Operators, or NCO, are a suite of file operators which facilitate manipulation and analysis of self-describing data stored in the (freely available) netCDF and HDF formats."



Funannotate is a pipeline for genome annotation originally designed for use with fungi genomes, but it can also be applied for other eukaryotes.