Welcome to Japsa

Japsa is a Java Package for Sequence Analysis. As the name implies, Japsa was written primarily in Java. It contains a large number of ready to run programs as well as a Java API.

Installation and Usage

Quick installation guide:

git clone https://github.com/mdcao/japsa
cd japsa
make install \
  [INSTALL_DIR=~/.usr/local \] 
  [MXMEM=7000m \] 
  [SERVER=true \] 
  [JLP=/usr/lib/jni:/usr/lib/R/site-library/rJava/jri]

Details of installation (including for Windows) and usage of Japsa can be found in its documentation hosted on ReadTheDocs

Authors and Contributors

Japsa was mainly developed and curated by Minh Duc Cao (@mdcao). The following people have contributed to the development of Japsa, including ideas, algorithms, implementation, documentation and feedback:

• Lachlan Coin
• Son Hoang Nguyen
• Mikael Boden
• Lloyd Allison
• Trevor I Dix
• Hoang Anh Nguyen
• Julia Bernal
• David Powell

License

Japsa is released under the accompanying BSD-like license.