pasa_cpp
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To build pasa, just type 'make' in this directory. An executable 'pasa' will be created. The pasa program accepts a text file as an input parameter, and this file must have the following format: accession,orientation,coordset1,coordset2,...[coordsetN] For example: acc1,+,100-200,300-500 acc2,+,300-500,700-800 acc3,+,750-850,950-1000 Only alignments with the same orientation can be assembled if they are found to be compatible (overlap with identical introns). There are several sample input files available for testing the pasa program, and each is a genuine example containing overlapping Arabidopsis transcript alignments. See pasa_cpp_sample_input* files. Questions, comments, or bug reports can be sent to Brian Haas ([email protected]) This software is freely available and open source. ------------------------------------------------------------------------- This software is provided "AS IS". TIGR makes no warranties, express or implied, including no representation or warranty with respect to the performance of the software and derivatives or their safety, effectiveness, or commercial viability. TIGR shall not be liable for any claim, demand or action for any loss, harm, illness or other damage or injury arising from access to or use of the software or associated information, including without limitation any direct, indirect, incidental, exemplary, special or consequential damages. -------------------------------------------------------------------------