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+.. _faq:
+
+
+FAQ
+===
+
+**Does ClipKIT trim amino acids, nucleotides, or codons?**
+
+ClipKIT trims amino acid and nucleotide alignments. Currently, ClipKIT does not trim codons. 
+
+|
+
+**Is there a website application of ClipKIT?**
+
+Currently, ClipKIT is only a command line tool.
+
+|
+
+**If tree inference with no trim works well, why even trim?**
+
+Tree inference with trimmed multiple sequence alignments is computationally efficient.
+In other words, shorter alignments require less computational time and memory during tree
+search. We found that ClipKIT reduced computation time by an average of 20%. As datasets
+continuously become bigger, an alignment trimming algorithm that can reduce computational
+time will be of great value. 
+
+|
+
+**I am having trouble install ClipKIT, what should I do?**
+
+Please install ClipKIT using a virtual environment as directed in the installation instructions.
+If you are still running into issues after installing in a virtual environment, please contact the
+main software developer via email_ or twitter_.
+
+.. _email: https://jlsteenwyk.com/contact.html
+.. _twitter: https://twitter.com/jlsteenwyk
+
+^^^^^