Mercurial > repos > padge > clipkit
comparison clipkit_repo/docs/frequently_asked_questions/index.rst @ 0:49b058e85902 draft
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
| author | padge |
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| date | Fri, 25 Mar 2022 13:04:31 +0000 |
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| 1 .. _faq: | |
| 2 | |
| 3 | |
| 4 FAQ | |
| 5 === | |
| 6 | |
| 7 **Does ClipKIT trim amino acids, nucleotides, or codons?** | |
| 8 | |
| 9 ClipKIT trims amino acid and nucleotide alignments. Currently, ClipKIT does not trim codons. | |
| 10 | |
| 11 | | |
| 12 | |
| 13 **Is there a website application of ClipKIT?** | |
| 14 | |
| 15 Currently, ClipKIT is only a command line tool. | |
| 16 | |
| 17 | | |
| 18 | |
| 19 **If tree inference with no trim works well, why even trim?** | |
| 20 | |
| 21 Tree inference with trimmed multiple sequence alignments is computationally efficient. | |
| 22 In other words, shorter alignments require less computational time and memory during tree | |
| 23 search. We found that ClipKIT reduced computation time by an average of 20%. As datasets | |
| 24 continuously become bigger, an alignment trimming algorithm that can reduce computational | |
| 25 time will be of great value. | |
| 26 | |
| 27 | | |
| 28 | |
| 29 **I am having trouble install ClipKIT, what should I do?** | |
| 30 | |
| 31 Please install ClipKIT using a virtual environment as directed in the installation instructions. | |
| 32 If you are still running into issues after installing in a virtual environment, please contact the | |
| 33 main software developer via email_ or twitter_. | |
| 34 | |
| 35 .. _email: https://jlsteenwyk.com/contact.html | |
| 36 .. _twitter: https://twitter.com/jlsteenwyk | |
| 37 | |
| 38 ^^^^^ |