Selecting a package name in the left column of the table expands the
entry with a short description. A green icon links to the home page of
the software. Any pages describing a given installation are linked from
the corresponding available version.
| | | gardar | hexagon | njord | stallo | titan | vilje |
|---|
| 454apps |  | | | | | 2.6
2.5.3
2.3
2.0.01.12
1.1.03.24
| |
|
| asreml | | | | | | 2.00ah
| |
| ASReml is a statistical software package for fitting linear mixed models using restricted maximum likelihood, a technique commonly used in plant and animal breeding and quantitative genetics as well as other fields. It is notable for its ability to fit very large and complex data sets efficiently, due to its use of the average information algorithm and sparse matrix methods. |
| BLAST | | | | | blast-2.2.19
blast-2.2.18
| 2.2.25
2.2.18
| |
| Searches a protein or DNA sequence data bank. |
| breve | | | | | | 2.7
2.4.1
| |
| A 3d Simulation Environment for
Multi-Agent Simulations and Artificial Life |
| ClustalW | | | | | 2.0.10
| 2.0.9
| |
| Clustal W is a general purpose multiple sequence alignment program for DNA or proteins.It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. |
| ClustalW-MPI | | | | | 0.13
| | |
| A Parallel Implementation of ClustalW, based on MPI. See also ClustalW. |
| cp2k | | | | | 2.0
| 8.12.2011
31.03.2011
| |
| CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. |
| EMBOSS | | | | | | 6.4.0
4.1.0
| |
| Package for seqence analysis. Tools for molecular biology |
| ePCR | | | | | | svn
| |
|
| Fasta | | | | | 36.3.4
35.4.7
| | |
| Searches a protein or DNA sequence data bank. |
| fastx | | | | | | 0.0.10
| |
| The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. |
| freesurfer | | | | | 5.1.0
4.2.0
4.0.4
| | |
| FreeSurfer is a set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface. |
| FSL | | | | | 4.1.6
4.1.4
4.1.2
4.0.4_64
4.0.2
| 4.1.7
4.1.2
| |
| FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. |
| garli | | | | | | 1.0
0.94
| |
|
| glimmer | | | | | 3.02
| | |
| Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. |
| GROMACS | | | | 4.5
4.0.5
3.3.3
| 4.0.5
3.3.3
| 4.5.3
| |
| Package for molecular dynamics. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. GROMACS |
| HMMER | | | | | hmmer-3.0rc2
| 3.0
2.3.2
| |
| Profile hidden Markov models. HMMER is an implementation of profile HMM methods for sensitive database searches using multiple sequence alignments as queries. Basically, you give HMMER a multiple sequence alignment as input; it builds a statistical model called a \"hidden Markov model\" which you can then use as a query into a sequence database to find (and/or align) additional homologues of the sequence family. HMMER |
| mafft | | | | | | 6.851
6.833
6.811
6.603
| |
| MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. |
| MEME | | | 4.4.0-intel
4.4.0-gnu
| | | 4.6.0
| |
|
| mpiBLAST | | | | 1.6.0.b1
| 1.5.0-pio
| 1.6.0
| |
| Searches a protein or DNA sequence data bank. BLAST |
| muscle | | | | | | 3.7
| |
|
| NAMD | | | 2.8b1
2.8
| 2.7
2.6
| 2.7b1
2.6-TCP
2.6
| | |
| NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.
|
| newbler | | | | | | 2.6
2.5.3
2.3
2.0.01.12
1.1.03.24
| |
| Newbler is a software package for de novo DNA sequence assembly. It is designed specifically for assembling sequence data generated by the 454 GS-series of pyrosequencing platforms sold by 454 Life Sciences, a Roche Diagnostics company. |
| openbugs | | | | | | 3.2.1
| |
| BUGS is a software package for performing Bayesian inference Using Gibbs Sampling. The user specifies a statistical model, of (almost) arbitrary complexity, by simply stating the relationships between related variables. The software includes an ‘expert system’, which determines an appropriate MCMC (Markov chain Monte Carlo) scheme (based on the Gibbs sampler) for analysing the specified model. The user then controls the execution of the scheme and is free to choose from a wide range of output types. |
| phredphrapconsed | | | | | | 1.0
2.0
| |
| The phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base. |
| Phylip | | | | | 3.68
| | |
| PHYLIP is a free package of programs for inferring phylogenies. It is distributed as source code, documentation files, and a number of different types of executables. Phylip |
| phylobayes | | | | | | 3.3b
3.2d
3.2e
| |
| PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments. Compared to other phylogenetic MCMC samplers (e.g. MrBayes), the main distinguishing feature of PhyloBayes is the underlying probabilistic model, CAT. It is particularly well suited for large multigene alignments, such as those used in phylogenomics. |
| phyml | | | | | | 3.vector
3.0
2.4.5
| |
| A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. |
| plink | | | | | | 1.07
1.06
1.05
| |
|
| poy | | | | | | 4.1.1
| |
|
| pyronoise | | | | | | 2
| |
| Software for Pyrosequencing Noise Removal |
| RAxML | | | | | | 7.2.6
7.0.4
| |
| RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum
Likelihood based inference of large phylogenetic trees. It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein’s dnaml which is part of the PHYLIP package. |
| structure | | | | | 2.3.1
| 2.2.3
2.3.3
2.2.2
| |
|
| tinker | | | | | 5.1
| | |
| The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. |
| UNPHASED | | | | | | 3.0.13
3.0.10
| |
| Software for genetic association analysis. |
