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bali_score evaluation program
(version 4.0, Jan 2011)
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This README contains help with INSTALLATION
Please e-mail bug reports/complaints/suggestions to
Julie Thompson at julie@igbmc.fr
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Compilation:
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First of all, you need the expat XML parser installed on your machine. If
this is not already done, you can get the parser from http://expat.sourceforge.net/
You should then edit the makefile supplied, changing the EXPAT_INC and EXPAT_LIB paths for your
system.
You make the program with:
make -f makefile
This produces the executable files bali_score bali_score_block bali_score_reliable.
Usage:
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To calculate overall column score (CS):
Usage: bali_score ref_aln test_aln
where ref_aln reference alignment in xml format
test_aln test alignment in msf or fasta format
To calculate individual block column scores (BCS):
Usage: bali_score_block ref_aln test_aln
where ref_aln reference alignment in xml format
test_aln test alignment in msf or fasta format
To calculate overall column score (CS), ignoring sequences with discrepencies (annotated with SEQERR features):
Usage: bali_score_reliable ref_aln test_aln
where ref_aln reference alignment in xml format
test_aln test alignment in msf or fasta format