T-Coffee is a versatile tool for making multiple sequence alignments. Its aim is to combine heterogeneous sources of information. The current implementation has been especially designed for combining local and global alignments, respectively from ClustalW and Lalign. It can also be used to combine a series of alternative multiple sequence alignments of the same sequences.
TransDecoder is software for identifying candidate coding regions within transcript sequences, including those from de novo RNA-Seq transcript assembly via Trinity, or from RNA-Seq alignments to the genome using Tophat and Cufflinks.
Trinotate is a transcriptome annotation suite designed for use with de novo assembled transcriptomes from model or non model organisms.
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."
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."
Globus is a data transfer service designed for convenient, fast file transferes between computer systems. More information about using Globus on MSI can be found here . These command line tools provide an alternative interface to the Globus functionality.
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."
From the NCCL website: NCCL (pronounced "Nickel") is a stand-alone library of standard collective communication routines, such as all-gather, reduce, broadcast, etc., that have been optimized to achieve high bandwidth over PCIe. NCCL supports an arbitrary number of GPUs installed in a single node and can be used in either single- or multi-process (e.g., MPI) applications.
UnRar is a utility for extracting WinRar archives (.rar files).
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.