Muscle
Muscle is a program for fast, high-quality multiple sequence alignment (MSA).
Contents
Experts
No experts have currently registered expertise on this specific subject. List of registered field experts:
| Field | AE FTE | General activities | ||
|---|---|---|---|---|
| Anders Hast (UPPMAX) | UPPMAX | Visualisation, Digital Humanities | 30 | Software and usability for projects in digital humanities |
| Anders Sjölander (UPPMAX) | UPPMAX | Bioinformatics | 100 | Bioinformatics support and training, job efficiency monitoring, project management |
| Anders Sjöström (LUNARC) | LUNARC | GPU computing MATLAB General programming Technical acoustics | 50 | Helps users with MATLAB, General programming, Image processing, Usage of clusters |
| Birgitte Brydsö (HPC2N) | HPC2N | Parallel programming HPC | Training, general support | |
| Björn Claremar (UPPMAX) | UPPMAX | Meteorology, Geoscience | 100 | Support for geosciences, Matlab |
| Björn Viklund (UPPMAX) | UPPMAX | Bioinformatics Containers | 100 | Bioinformatics, containers, software installs at UPPMAX |
| Chandan Basu (NSC) | NSC | Computational science | 100 | EU projects IS-ENES and PRACE. Working on climate and weather codes |
| Diana Iusan (UPPMAX) | UPPMAX | Computational materials science Performance tuning | 50 | Compilation, performance optimization, and best practice usage of electronic structure codes. |
| Frank Bramkamp (NSC) | NSC | Computational fluid dynamics | 100 | Installation and support of computational fluid dynamics software. |
| Hamish Struthers (NSC) | NSC | Climate research | 80 | Users support focused on weather and climate codes. |
| Henric Zazzi (PDC) | PDC | Bioinformatics | 100 | Bioinformatics Application support |
| Jens Larsson (NSC) | NSC | Swestore | ||
| Jerry Eriksson (HPC2N) | HPC2N | Parallel programming HPC | HPC, Parallel programming | |
| Joachim Hein (LUNARC) | LUNARC | Parallel programming Performance optimisation | 85 | HPC training Parallel programming support Performance optimisation |
| Johan Hellsvik | PDC | Materialvetenskap | 30 | materials theory, modeling of organic magnetic materials, |
| Johan Raber (NSC) | NSC | Computational chemistry | 50 | |
| Jonas Lindemann (LUNARC) | LUNARC | Grid computing Desktop environments | 20 | Coordinating SNIC Emerging Technologies Developer of ARC Job Submission Tool Grid user documentation Leading the development of ARC Storage UI Lunarc Box Lunarc HPC Desktop |
| Krishnaveni Chitrapu (NSC) | NSC | Software development | ||
| Lars Eklund (UPPMAX) | UPPMAX | Chemistry Data management FAIR Sensitive data | 100 | Chemistry codes, databases at UPPMAX, sensitive data, PUBA agreements |
| Lars Viklund (HPC2N) | HPC2N | General programming HPC | HPC, General programming, installation of software, support, containers | |
| Lilit Axner (PDC) | PDC | Computational fluid dynamics | 50 | |
| Marcus Lundberg (UPPMAX) | UPPMAX | Computational science Parallel programming Performance tuning Sensitive data | 100 | I help users with productivity, program performance, and parallelisation. I also work with allocations and with sensitive data questions |
| Martin Dahlö (UPPMAX) | UPPMAX | Bioinformatics | 10 | Bioinformatic support |
| Matias Piqueras (UPPMAX) | UPPMAX | Humanities, Social sciences | 70 | Support for humanities and social sciences, machine learning |
| Mikael Djurfeldt (PDC) | PDC | Neuroinformatics | 100 | |
| Mirko Myllykoski (HPC2N) | HPC2N | Parallel programming GPU computing | Parallel programming, HPC, GPU programming, advanced support | |
| Pavlin Mitev (UPPMAX) | UPPMAX | Computational materials science | 100 | |
| Pedro Ojeda-May (HPC2N) | HPC2N | Molecular dynamics Machine learning Quantum Chemistry | Training, HPC, Quantum Chemistry, Molecular dynamics, R, advanced support | |
| Peter Kjellström (NSC) | NSC | Computational science | 100 | All types of HPC Support. |
| Peter Münger (NSC) | NSC | Computational science | 60 | Installation and support of MATLAB, Comsol, and Julia. |
| Rickard Armiento (NSC) | NSC | Computational materials science | 40 | Maintainer of the scientific software environment at NSC. |
| Szilard Pall | PDC | Molecular dynamics | 55 | Algorithms & methods for accelerating molecular dynamics, Parallelization and acceleration of molecular dynamics on modern high performance computing architectures, High performance computing, manycore and heterogeneous architectures, GPU computing |
| Thomas Svedberg (C3SE) | C3SE | Solid mechanics | ||
| Torben Rasmussen (NSC) | NSC | Computational chemistry | 100 | Installation and support of computational chemistry software. |
| Wei Zhang (NSC) | NSC | Computational science Parallel programming Performance optimisation | code optimization, parallelization. | |
| Weine Olovsson (NSC) | NSC | Computational materials science | 90 | Application support, installation and help |
| Åke Sandgren (HPC2N) | HPC2N | Computational science | 50 | SGUSI |
Availability
| Resource | Centre | Description |
|---|---|---|
| Kappa | NSC | throughput cluster resource of 26 TFLOPS |
| Matter | NSC | cluster resource of 37 TFLOPS dedicated to materials science |
License
License: Free.
Any further license particularities (such as site licenses) are succinctly described here.
Compilation
Benchmarks at NSC have shown that Intel compilers seem to produce more efficient Muscle binaries than does gcc, and in particular when using interprocess optimisations (-ipo), which can more than double the execution speed.
However, as Muscle relies heavily on floating point arithmetics, and as such is sensitive to subtle changes in architecture and compiler versions, the alignments produced may not be identical to the ones produced by the official gcc-built binary distribution. The discrepancies have been noted and judged non-critical by NSC and Robert Edgar (author of the Muscle software), but if you rely on bit equivalence in the results, you should use the official precompiled binary distribution instead.
That said, a freely distributable binary release compiled at NSC with icpc -O3 -ipo -static is available for download here: File:Muscle3.8.31-nsc1 i86linux64.tar.gz. See README.TXT for licence and details.
