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The source posted on the Mothur page at http://www.mothur.org/wiki/Download_Clearcut
is identical to the upstream bar this one change.
I have not investigated why, but I assume it's there for a reason and
QIIME says it wants the Mothur version.
--- a/clearcut.c
+++ b/clearcut.c
@@ -1494,7 +1494,7 @@
}
NJ_output_tree2(fp, nj_args, tree, tree, dmat);
- fprintf(fp, " ;\n");
+ fprintf(fp, ";\n");
if(!nj_args->stdout_flag) {
fclose(fp);
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