| [HMMER](http://hmmer.org/) | HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST. |
| [HMMER](http://hmmer.org/) | HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST. |
| [Kalign](https://github.com/TimoLassmann/kalign) | Kalign is a fast multiple sequence alignment program for biological sequences. |
| [Kalign](https://github.com/TimoLassmann/kalign) | Kalign is a fast multiple sequence alignment program for biological sequences. |
| [MaSuRCA](http://www.genome.umd.edu/masurca.html) | MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore). |
| [MaSuRCA](http://www.genome.umd.edu/masurca.html) | MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore). |
| [OpenMM](https://openmm.org) | OpenMM is a toolkit for molecular simulation. |
| [picard](https://broadinstitute.github.io/picard/) | A set of tools (in Java) for working with next generation sequencing data in the BAM format. |
| [picard](https://broadinstitute.github.io/picard/) | A set of tools (in Java) for working with next generation sequencing data in the BAM format. |
| [RELION](http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page) | RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). |
| [RELION](http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page) | RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). |
| [Salmon](https://github.com/COMBINE-lab/salmon) | Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. |
| [Salmon](https://github.com/COMBINE-lab/salmon) | Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. |