Hasstedt > jPAP (Pedigree Analysis Package for Java)

Description

This dramatically revised edition of Pedigree Analysis Package (PAP) is of modular design and features a document-driven GUI. The package provides a powerful framework for genetic analysis, centered around computation of likelihoods on pedigree members using genetic models. jPAP may be used for segregation analysis, variance components analysis, linkage analysis, measured genotype analysis, transmission disequilibrium testing, or genetic model fitting.

System Requirements

A Java runtime must be present on the target system, specifically a runtime implementing J2SE version 1.4.x or greater. Runtimes for Linux, Solaris, and Windows are freely available from Sun Microsystems. Runtimes are available for other major OSes as well, typically through the OS vendor.

Because jPAP 1.x is a transitional implementation that includes a residual native engine, there are additional requirements beyond those imposed by the Java environment. Most notably, at least a gigabyte of RAM is required to run commands in jPAP without adjusting default virtual memory settings. (Such an adjustment is OK if necessary for temporary demo purposes, but is not recommended for long term use, especially on Windows, since it may degrade system performance.) Another consequence of the current jPAP's hybrid nature is that our distribution bundles must be platform-specific. (The "etcix" edition, which contains sources rather than binaries for the native components, is a partial exception, but it requires native build tools, including a Fortran 77 compatible compiler, and is still rather tailored to a unix-style system.)

Documentation

Documentation is included in the download bundles, and may also be browsed online via the links below.

Download

jPAP v1.5.1 July 25, 2007

jPAP remains under continuous development; updates are posted as significant features are added or bugs fixed. See the change log for details on per-version modifications. Note: some simple "demo" project files are integrated into the application bundle.

Platform-specific bundles:

Generic bundle (Fortran compiler required):

jPAP v1.5.1 Unix-style systems [tar.gz] - 1.0 MB

jPAP v1.4.0 (Feb 23, 2006)

Platform-specific bundles:

Generic bundle (Fortran compiler required):

jPAP v1.4.0 Unix-style systems [tar.gz] - 1.0 MB

Example Files Used in the jPAP Tutorial at IGES 2005 - Updated for jPAP 1.5

Bundled for Linux/Unix [tar.gz] - 134 KB
Bundled for Windows [zip] - 237 KB
PowerPoint Presentation - PowerPoint presentation that accompanies the tutorial examples.

Special Announcements

jPAP News RSS feed

Since there are periods when jPAP receives frequent updates, we offer an

feed of jPAP news. Subscribers will receive a brief notice of each incremental update at the time it is posted, as well as other jPAP-related announcements. (For information about web-feed technology and clients that support it, such as Mozilla.org's Thunderbird and Firefox, see the Wikipedia article on RSS.)