Can any one please tell me if we can view alignment between the query and the hits obtained when using cd-hit-est-2d. It is difficult to guess the position of mismatches and gaps using the current format.
Thanks in advance!!
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jaspreetk.dhanjal •
No, not really this option. What I need is a detailed alignment between the query and the hits obtained showing the position of matches, mismatches and gaps.
Not very well documented (i.e. at all), but to see the alignments, apparently you have to compile cd-hit yourself with MAKEALIGN macro defined. How to define it? I have no clue..
I found this post but it does not work. Nothing more is available in the same context.
Post your issue to https://github.com/weizhongli/cdhit/issues
Thanks a lot for the suggestion!
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