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How do I get log file and qscores from clustalw2?

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How do I get log file and qscores from clustalw2?

Postby madriley » Sun Nov 28, 2010 6:27 am

I am writing a java program that runs a command line version of clustal in the background and reads in the input.

Here is an example of one of my command lines:
ClustalW2.exe "/infile=d:\bioinformatics\clustal\ClustalW2\seqcytochrome oxidase subunit 1.input" "/outfile=d:\bioinformatics\clustal\ClustalW2\seqcytochrome oxidase subunit 1.output" /o
utput=FASTA

This produces the aligned sequences and the guide tree, but I can't figure out how to produce a log file showing the pairwise scores and the qscores files that you can easily get from clustalx by choosing "Save Column Scores To File" from the quality menu. Does anyone know how to produce this file from the command line???
Thanks in advance!!
madriley
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