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planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
author iuc
date Sun, 09 Nov 2025 10:56:06 +0000
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a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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1 <macros>
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2 <token name="@TOOL_VERSION@">14.1</token>
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3 <token name="@WRAPPER_VERSION@">0</token>
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4 <xml name="help">
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5 <help><![CDATA[
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6 **Overview**
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a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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8 PAL2NAL converts a protein multiple sequence alignment plus the matching nucleotide FASTA records into a codon-aware alignment suitable for downstream Ka/Ks analyses. The script is maintained by Mikita Suyama (Kyushu University) and is distributed under GPL v2. This Galaxy wrapper surfaces the upstream `pal2nal.pl` tool so that codon alignments can be created inside workflows.
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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10 **Inputs**
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a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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12 * *Protein alignment (pep.aln)* — CLUSTAL or FASTA alignment of the translated sequences. Alignments may contain more than two sequences, and frame-shift events can be annotated by numeric placeholders (for example, `2` indicates a single base deletion; see the bundled `test.aln` example).
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13 * *Nucleotide FASTA (nuc.fasta)* — Corresponding DNA or mRNA sequences. Attach one or more FASTA datasets (use *Add new Nucleotide FASTA files* for additional inputs). Sequence identifiers must match those in the protein alignment; order is detected automatically when identifiers match.
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15 **Options**
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17 * `-output clustal|paml|fasta|codon` (Galaxy: *Output format*).
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18 * `-blockonly` — Restrict output to user-marked blocks (`#` rows in CLUSTAL alignments).
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19 * `-nogap` — Remove codons containing gaps or in-frame stops.
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20 * `-nomismatch` — Remove codons where amino acid and nucleotide sequences disagree (useful for discarding pseudogene regions).
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21 * `-codontable` — Choose an NCBI genetic code (1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23).
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22 * `-html` — Produce HTML formatted output (Galaxy: enable *Add HTML formatted output* to store the optional HTML view).
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23 * `-nostderr` — Suppress STDERR warnings (for example, expected pseudogene mismatches).
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25 **Outputs**
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27 * Codon-respecting alignment rendered in the selected format (Galaxy labels the dataset as CLUSTAL, PAML, FASTA, HTML, or plain text as appropriate).
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a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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29 **Example:**
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a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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31 ```pal2nal.pl inputs/test.aln inputs/test.nuc -output paml -nogap > inputs/for_paml/test.codon```
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33 **Ka/Ks calculation**
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35 To compute Ka and Ks values, run the resulting codon alignment through PAML's `codeml`, as illustrated in the PAL2NAL distribution (`inputs/for_paml/test.cnt`, `test.tree`, `test.codeml.ori`).
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37 **Warnings**
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39 PAL2NAL issues messages when protein residues and underlying codons disagree (for example, pseudogene cases). These warnings are harmless unless they indicate unintended mismatches; enable *Suppress STDERR messages* to hide them.
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41 **References and contacts**
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43 * PAL2NAL website: http://www.bork.embl.de/pal2nal
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44 * Support: Mikita Suyama (mikita@bioreg.kyushu-u.ac.jp)
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45 * Example data: `inputs/test.aln`, `inputs/test.nuc`, and PAML helpers inside the `inputs/for_paml/` directory.
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46 ]]></help>
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47 </xml>
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48 <xml name="citations">
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49 <citations>
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50 <citation type="doi">10.1093/nar/gkl315</citation>
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51 </citations>
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52 </xml>
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53 </macros>