Muscle
From SNIC Documentation
Muscle is a program for fast, high-quality multiple sequence alignment (MSA).
Contents |
Availability
| Resource | Centre | Description |
|---|---|---|
| Kappa | NSC | throughput cluster resource of 26 TFLOPS |
| Matter | NSC | cluster resource of 37 TFLOPS dedicated to materials science |
| Neolith | NSC | capability cluster resource of 60 TFLOPS with full bisection infiniband interconnect |
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.
Experts
No experts have currently registered expertise on this specific subject. List of registered field experts:| Field | AE FTE | General activities | ||
|---|---|---|---|---|
| Joel Hedlund (NSC) | NSC | Bioinformatics | 5050 | BILS computing service portal development. Snicdocs development. |
| Martin Dahlö (UPPMAX) | UPPMAX | Bioinformatics | 1010 | Bioinformatic support |
| Pall Isolfur Olason (UPPMAX) | UPPMAX | Bioinformatics | 5050 | High throughput sequencing analysis. |
| Samuel Lampa (UPPMAX) | UPPMAX | Bioinformatics | 100100 | Automated data handling for NextGen Sequencing data, Graphical HPC clients. |
