i am using Bali_score to analize multiple protein sequence alignment using the BaliBase RV11 set. It runs on Biolinux and aparently reads the xml reference alignment and the fasta test alignment.
But it always produces a 0.0 score. I tried making an false evaluation from two identical alignments, (expecting a high score as a test) but it keeps producing 0.0 score and no error mesage
Dear Ernesto,
You can try this C implementation:
http://prodata.swmed.edu/download/pub/PCMA/evalscore/baliscore.c
Just compile it and run on linux terminal. However, it expects a MSF format for both alignment and reference file.
Best regards.
Thanks Amorim it will be useful, also found QScore and Mumsa programs for this task. Now i need to convert many files from MSF to Fasta anda viceversa. I tried in Galaxy and others but MSF seems to be uncommon. Do you know some way?
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