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annotate clipkit_repo/docs/frequently_asked_questions/index.rst @ 0:49b058e85902 draft

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"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
author padge
date Fri, 25 Mar 2022 13:04:31 +0000
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1 .. _faq:
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4 FAQ
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5 ===
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7 **Does ClipKIT trim amino acids, nucleotides, or codons?**
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9 ClipKIT trims amino acid and nucleotide alignments. Currently, ClipKIT does not trim codons.
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13 **Is there a website application of ClipKIT?**
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15 Currently, ClipKIT is only a command line tool.
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19 **If tree inference with no trim works well, why even trim?**
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21 Tree inference with trimmed multiple sequence alignments is computationally efficient.
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22 In other words, shorter alignments require less computational time and memory during tree
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23 search. We found that ClipKIT reduced computation time by an average of 20%. As datasets
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24 continuously become bigger, an alignment trimming algorithm that can reduce computational
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25 time will be of great value.
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29 **I am having trouble install ClipKIT, what should I do?**
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31 Please install ClipKIT using a virtual environment as directed in the installation instructions.
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32 If you are still running into issues after installing in a virtual environment, please contact the
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33 main software developer via email_ or twitter_.
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35 .. _email: https://jlsteenwyk.com/contact.html
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36 .. _twitter: https://twitter.com/jlsteenwyk
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38 ^^^^^