A terminal-based app for genotyping via complete composition vectors and mapreduce #Complete composition vectors #Mapreduce genotyping #Vector algorithm #CCV #Vector #Mapreduce
The classic genotyping approach has been based on phylogenetic analysis, starting with a multiple sequence alignment. Genotypes are then established by expert examination of phylogenetic trees.
However, such methods are suboptimal for a rapidly growing dataset, because they require significant human effort, and because they increase in computational complexity quickly with the number of sequences.
CompleteCompositionVectorCLI employs a method for genotyping which is independent of any multiple sequence alignment.
CompleteCompositionVectorCLI uses the complete composition vector algorithm to represent each sequence in the dataset as a vector derived from its constituent k-mers, and affinity propagation clustering to group the sequences into genotypes based on a distance measure over the vectors.
Our methods produce results that correlate well with expert-defined clades or genotypes, at a fraction of the computational cost of traditional phylogenetic methods.
Detailed instructions on how to install and use the CompleteCompositionVectorCLI utility on your Mac are available HERE.
System requirements
CompleteCompositionVectorCLI 2.2.1 Build 6
add to watchlist add to download basket send us an update REPORT- runs on:
- Mac OS X (-)
- file size:
- 26.7 MB
- filename:
- ccv-2.2.1.tar.gz
- main category:
- Math/Scientific
- developer:
- visit homepage
IrfanView
Context Menu Manager
Microsoft Teams
Bitdefender Antivirus Free
ShareX
Windows Sandbox Launcher
calibre
7-Zip
4k Video Downloader
Zoom Client
- 7-Zip
- 4k Video Downloader
- Zoom Client
- IrfanView
- Context Menu Manager
- Microsoft Teams
- Bitdefender Antivirus Free
- ShareX
- Windows Sandbox Launcher
- calibre