BSD Portsbiology/spoa 4.1.0 DragonFly
C++ implementation of the partial order alignment (POA) algorithm
- System
- DragonFly
- Repository
- DPorts
- Maintainer
- [email protected] (as in FreeBSD)
- License
- MIT
- Categories
- biology
- Package size
- 78.3 KiB, 317.6 KiB installed
Description
Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which is used to generate consensus sequences. It supports three alignment modes: local (Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment (overlap), and three gap modes: linear, affine and convex (piecewise affine). It also supports Intel SSE4.1+ and AVX2 vectorization (marginally faster due to high latency shifts), SIMDe and dispatching.
In the other systems
The newest version among them is 4.1.5, as upstream numbers it.
| System | Port | Version | Vulnerabilities | Status | Maintainer | Last update |
|---|---|---|---|---|---|---|
| DragonFly | biology/spoa | 4.1.0 | none known | - | [email protected] | - |
| FreeBSD | biology/spoa | 4.1.5 newest | none known | - | [email protected] | - |
| HardenedBSD | biology/spoa | 4.1.5 newest | no data | - | [email protected] | - |
| GhostBSD | biology/spoa | 4.1.5 newest | no data | - | [email protected] | - |
Install
Binary package:
pkg install spoaFrom DPorts:
cd /usr/dports/biology/spoa && make install cleanDependency graph
Ports that need it on the left, what it needs to run on the right; at most 8 of each. "Dependencies" below lists them all.
Dependencies
Run dependencies 2
No port depends on this one.