Sarment


Sarment is a source package of object-oriented Python modules for sequence segmentation via HMM analysis and Maximal Predictive Partitioning.

Sarment is under GPL license.

It provides several classes:

Data storage and heavy computation are written in C++, to limit memory use and time consumption. Then, compilation process is needed to install Sarment.

Downloading Sarment

10/29/2008: New version, number 5. All the files for version 4 are here , and for version 3, here .

Sarment is available for UNIX, LINUX or MacOS X operating systems. It needs Python version 2.(>=2).
Makefile is made for GNU make and compilation needs g++ version >=2.95.

Compilation needs Python headers files. The header files are typically installed with Python.

Untarify this archive wherever you want, and do not forget to update PYTHONPATH environment variable.

Sarment sources can be downloaded in tar gz.

Several headers locations are tested during make operation (see top of the makefile), but perhaps yours is not included. In that case, uncomment INC definition and add the correct location.

For compilation, just do "make".
During compilation, a link to the "right" header directory is made in SrcCPP directory, with name Pythondev. If the link is not correct, either delete it before recompilating, or change it to the correct directory.

Afterwards, "make exec" tarifies in Sarment.tar all the files that are necessary for usage.
Untarify this file wherever you want, and do not forget to update PYTHONPATH environment variable.

Using Sarment

The version of python to be used depends on your system, which determines the link of Pythondev in SrcCPP directory.

For the use of these classes, there is a manual in html or pdf .

To facilitate the usage of these classes, there is a tutorial in html or pdf .

Reference

Sarment: Python modules for HMM analysis and partitioning of sequences. Guéguen, L. Bioinformatics. 2005 Aug 15;21(16):3427-8 http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/16/3427?etoc

If you encounter some problems when using Sarment, please contact Laurent Guéguen. Any comments or suggestions are welcome.


If you have problems or comments...

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