Tag: PRIME

PrIME 1.0.5 – Library and Accompanying tools for Phylogenetics

PrIME 1.0.5

:: DESCRIPTION

PrIME (Probabilistic Integrated Models of Evolution) is a library and accompanying tools for phylogenetics. PrIME mainly relies on Markov-chain Monte Carlo (MCMC) framework and probabilistic modeling.

::DEVELOPER

the Science for Life Laboratory, Uppsala University,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PrIME

:: MORE INFORMATION

Citation:

Integrating Sequence Evolution into Probabilistic Orthology Analysis.
Ullah I, Sjöstrand J, Andersson P, Sennblad B, Lagergren J.
Syst Biol. 2015 Nov;64(6):969-82. doi: 10.1093/sysbio/syv044

PRIME 0.9 – Mass Spectrum Data Mining Tool

PRIME 0.9

:: DESCRIPTION

PRIME (PaRtition of Ion types of tandem Mass spectra)is a software for identification of b and y ions in tandem mass spectra, a key challenging problem in de novo sequencing. PRIME utilizes a feature that ions of the same and different types follow different mass-difference distributions to separate b from y ions correctly. We have formulated the problem as a graph partition problem.A linear integer-programming algorithm has been implemented to solve the graph partition problem rigorously and efficiently.

::DEVELOPER

the Computational Systems Biology Laboratory at the University of Georgia 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 PRIME

:: MORE INFORMATION

Citation

B. Yan, Y. Qu, F. Mao, V Olman, Ying Xu,
PRIME: A Mass Spectrum Data Mining Tool for De Novo Sequencing and PTMs Identification
Journal of Computer Science and Technology