Changes from Version 1 of RunningPaircompLocally

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Author:
titus (IP: 131.215.34.153)
Timestamp:
04/04/06 12:51:08 (12 years ago)
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  • RunningPaircompLocally

    v v1  
     1= Running Paircomp Locally = 
     2 
     31. Download and compile paircomp locally: 
     4 
     5{{{ 
     6svn co http://svn.idyll.org/repos/cartwheel/trunk/paircomp paircomp 
     7cd paircomp 
     8make depend 
     9make 
     10}}} 
     11 
     122. Generate the comparison: 
     13 
     14{{{ 
     15bin/paircomp seq1.fasta seq2.fasta 20 0.7 seq1-seq2.cmp 
     16}}} 
     17 
     18Here '20' is the windowsize and 0.7 is the threshold to use. 
     19 
     203. Generate the 'sister' format XML file: 
     21 
     22{{{ 
     23scripts/paircomp-to-sister se1.fasta seq2.fasta 20 seq1-seq2.cmp seq1-seq2.xml 
     24}}} 
     25 
     26where '20' is again the windowsize. 
     27 
     28At this point you can use FamilyRelationsII to view the output file, e.g. 
     29 
     30{{{ 
     31/path/to/FRII/build/dir/app/view-sister seq1-seq2.xml 
     32}}}