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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit 4272ec0a9c9fc6c2a54aa702a3dc446ec598ffcc
author iuc
date Tue, 05 Aug 2025 20:08:31 +0000
parents c0a3b4607e66
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c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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1 <macros>
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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2 <token name="@TOOL_VERSION@">1.1.4</token>
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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3 <token name="@VERSION_SUFFIX@">0</token>
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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4 <xml name="requirements">
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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5 <requirements>
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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6 <requirement type="package" version="@TOOL_VERSION@">cialign</requirement>
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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7 </requirements>
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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8 </xml>
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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9 <xml name="help">
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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10 <help><![CDATA[
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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11 What this tool does
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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12 ===================
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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13
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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14 CIAlign is designed to clean, interpret, and visualize multiple sequence alignments (MSAs).
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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15 It helps identify and remove problematic regions such as insertions, poorly aligned ends, and overly gappy sequences. This improves downstream analyses like phylogenetic inference and comparative genomics.
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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16
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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17 It also offers tools to generate customizable visualizations, allowing users to inspect alignments and cleaning steps through compact and informative plots.
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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18
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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19 Input
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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20 =====
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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21
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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22 CIAlign takes standard multiple sequence alignment files in FASTA format. CIAlign takes standard multiple sequence alignment files in FASTA format.
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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23
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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24 Output
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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25 ======
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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26
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27 CIAlign produces a cleaned alignment in FASTA format along with optional log files, summary statistics, and visualization plots.
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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29 ]]></help>
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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30 </xml>
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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31 <xml name="creator">
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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32 <creator>
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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33 <organization name="Galaxy Europe"/>
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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34 <person givenName="Ahmad" familyName="Mahagna" url="https://github.com/Smkingsize"/>
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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35 <person givenName="Saim" familyName="Momin" url="https://github.com/SaimMomin12"/>
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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36 </creator>
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37 </xml>
c0a3b4607e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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38 </macros>