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annotate codeml.xml @ 1:5750c1f4b0eb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0
author iuc
date Wed, 02 May 2018 05:39:28 -0400
parents 6c12b9745b3e
children 853e3ce30204
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6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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1 <tool name="codeML" id="codeml" version="1.0">
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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2 <description>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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3 Detects positive selection (paml package)
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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4 </description>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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5
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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6 <macros>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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7 <import>macros.xml</import>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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8 </macros>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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9
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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10 <requirements>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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11 <requirement type="package" version="4.9">paml</requirement>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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12 </requirements>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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13
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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14 <version_command><![CDATA[ codeml /dev/null 2>&1 | tail -1 ]]></version_command>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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15
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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16 <command><![CDATA[
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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17 codeml '$codeml_ctl'
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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18 &&
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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19 mv '$codeml_ctl' '$ctl'
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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20 ]]></command>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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21
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22 <configfiles>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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23 <configfile name="codeml_ctl"><![CDATA[
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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24 seqfile = $concat_nuc * sequence data file name
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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25 outfile = run_codeml * main result file name
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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26 treefile = $tree * tree structure file name
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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27 noisy = 9 * 0,1,2,3,9: how much rubbish on the screen
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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28 verbose = $adv.verbose * 1: detailed output, 0: concise output
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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29 runmode = $adv.runmode * 0: user tree; 1: semi-automatic; 2: automatic
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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30 * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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31 seqtype = $adv.seqtype * 1:codons; 2:AAs; 3:codons-->AAs
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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32 CodonFreq = $adv.CodonFreq * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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33 clock = $adv.clock * 0:no clock, 1:clock; 2:local clock
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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34 aaDist = $adv.aaDist * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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35 * 7:AAClasses
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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36 aaRatefile = $adv.aaRateFile * only used for aa seqs with model=empirical(_F)
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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37 * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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38 model = $compat_model.brmodel
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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39 * models for codons:
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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40 * 0:one, 1:b, 2:2 or more dN/dS ratios for branches
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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41 * models for AAs or codon-translated AAs:
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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42 * 0:poisson, 1:proportional,2:Empirical,3:Empirical+F
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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43 * 6:FromCodon, 8:REVaa_0, 9:REVaa(nr=189)
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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44 NSsites = $compat_model.NSsites * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs;
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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45 * 5:gamma;6:2gamma;7:beta;8:beta&w;9:beta&gamma;
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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46 * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1;
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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47 * 13:3normal>0
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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48 icode = $adv.icode * 0:universal code; 1:mammalian mt; 2-11:see below
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49 Mgene = $adv.Mgene * 0:rates, 1:separate;
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50 fix_kappa = $adv.fix_kappa * 1: kappa fixed, 0: kappa to be estimated
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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51 kappa = $adv.kappa * initial or fixed kappa
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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52 fix_omega = $adv.fix_omega * 1: omega or omega_1 fixed, 0: estimate
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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53 omega = $adv.omega * initial or fixed omega, for codons or codon-based AAs
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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54 fix_alpha = $adv.fix_alpha * 0: estimate gamma shape parameter; 1: fix it at alpha
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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55 alpha = $adv.alpha * initial or fixed alpha, 0:infinity (constant rate)
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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56 Malpha = $adv.Malpha * 1: different alphas for genes, 0 : one alpha
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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57 ncatG = $adv.ncatG * # of categories in dG of NSsites models
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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58 fix_rho = $adv.fix_rho * 0: estimate rho; 1: fix it at rho
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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59 rho = $adv.rho * initial or fixed rho, 0:no correlation
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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60 getSE = $adv.getSE * 0: don't want them, 1: want S.E.s of estimates
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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61 RateAncestor = $adv.RateAncestor * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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62 Small_Diff = $adv.Small_Diff
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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63 cleandata = $adv.cleandata * remove sites with ambiguity data (1:yes, 0:no)?
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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64 fix_blength = $adv.fix_blength * 0: ignore, -1: random, 1: initial, 2: fixed
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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65 method = $adv.method * 0: simultaneous; 1: one branch at a time
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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66 ]]></configfile>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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67 </configfiles>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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68
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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69 <inputs>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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70 <param name="concat_nuc" type="data" format="fasta" label="Sequences file" help="The fasta file with the sequences to be analyzed" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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71 <param name="tree" type="data" format="nhx" label="tree file" help="Tree file in Newick format" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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72
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73 <conditional name="compat_model" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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74 <param argument="brmodel" type="select" label="Branch model ; for tree file editing in model 2 and 3, see paml manual (chap.3)" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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75 <option value="0" selected="true">'0' : one dN/dS ratio for all branches (e.g. basic model if NSsites=0)</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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76 <option value="1">'1' : one dN/dS ratio for each branch ("free-ratio model") ; its use is discouraged</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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77 <option value="2">'2' : arbitrary number of ratios ; implies to manually edit your tree file</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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78 <option value="3">'3' : clade-model ; implies to manually edit your tree file</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
79 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
80
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
81 <when value="0" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
82 <expand macro="FSsites_br0" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
83 </when>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
84 <when value="1">
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
85 <expand macro="FSsites_br1" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
86 </when>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
87 <when value="2" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
88 <expand macro="FSsites_br2_and_3" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
89 </when>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
90 <when value="3" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
91 <expand macro="FSsites_br2_and_3" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
92 </when>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
93 </conditional>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
94
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
95 <!-- advanced parameters -->
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
96 <section name="adv" title="Advanced Options" expanded="False" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
97 <param argument="verbose" type="select" label="Set the level of details in the log file">
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
98 <option value="0" selected="true">0 : concise output</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
99 <option value="1">1 : detailed output</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
100 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
101
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
102 <param argument="runmode" type="select" label="Tree analysis mode" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
103 <option value="0" selected="true">0 : user tree</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
104 <option value="1">1 : heuristic tree search starting from a multifurcating tree from the tree structure file</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
105 <option value="2">2 : heuristic tree search starting from the tree file</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
106 <option value="3">3 : StepwiseAddition</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
107 <option value="4">4 : PerturbationNNI with the starting tree obtained by a parsimony algorithm</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
108 <option value="5">5 : PerturbationNNI with the starting tree read from the tree structure file</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
109 <option value="-2">-2 : ML estimation of dS and dN in pairwise comparisons of protein-coding sequences</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
110 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
111
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
112 <param argument="seqtype" type="select" label="Sequences format in the fasta file" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
113 <option value="1" selected="true">1 : codons</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
114 <option value="2">2 : Amino acids (only compatible with FSsites=0) </option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
115 <option value="3">3 : codons--&gt;amino acids (only compatible with FSsites=0)</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
116 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
117
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
118 <param argument="CodonFreq" type="select" label="Equilibrium codon frequencies in codon substitution model">
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
119 <option value="0">0 : 1/61 each:</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
120 <option value="1" selected="true">1 : FIX4</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
121 <option value="2">2 : codon table</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
122 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
123
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
124 <param argument="clock" type="select" label="Specifies models concerning rate constancy or variation among lineages" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
125 <option value="0" selected="true">0 : no clock ; An unrooted tree should be used under this model</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
126 <option value="1">1 : clock</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
127 <option value="2">2 : local clock (needed : branch labels in the tree)</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
128 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
129
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
130 <param argument="aaDist" type="select" label="Amino acid distances" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
131 <option value="0" selected="true">0 : equal (warning : the only one compatible with NSsites and seqtype=codons</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
132 <option value="+">+ : geometric</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
133 <option value="-">- : linear</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
134 <option value="1">1 : G1974</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
135 <option value="2">2 : Miyata</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
136 <option value="3">3 : c</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
137 <option value="4">4 : p</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
138 <option value="5">5 : v</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
139 <option value="6">6 : a</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
140 <option value="7">7 : AAClasses</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
141 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
142
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
143 <param argument="aaRateFile" type="select" label="Amino acide substitution rate matrix" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
144 <option value="wag.dat" selected="true">wag.dat</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
145 <option value="dayhoff.dat">dayhoff.dat</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
146 <option value="jones.dat">jones.dat</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
147 <option value="mtmam.dat">mtmam.dat</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
148 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
149
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
150 <param argument="icode" type="select" label="Icode : specifies the genetic code" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
151 <option value="0" selected="true">0 : universal code</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
152 <option value="1">1 : mammalian mt</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
153 <option value="3">3 : mold mt</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
154 <option value="4">4 : invertebrate mt</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
155 <option value="5">5 : ciliate nuclear code mt</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
156 <option value="6">6 : echinoderm mt</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
157 <option value="7">7 : euplotid mt</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
158 <option value="8">8 : alternative yeast nuclear</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
159 <option value="9">9 : scidian mt</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
160 <option value="10">10 : blepharisma nuclear</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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161 <option value="11">11 : Yang's regularized code</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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162 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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163
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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164 <param argument="Mgene" type="select" value="0" label="Multiple genes"
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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165 help="Used in combination with option G in the sequence data file, for combined analysis of data from multiple genes or multiple site partitions" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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166 <option value="0">0 : complete homogeneity among genes </option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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167 <option value="1">1 : equivalent to a separate analysis</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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168 <option value="2">2 : different frequency parameters for different genes but the same rate ratio parameters</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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169 <option value="3">3 : different rate ratio parameters and the same frequency parameters</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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170 <option value="4">4 : both different rate ratio parameters and different frequency parameters for different genes </option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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171 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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172
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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173 <param argument="fix_kappa" type="select" label="Specifies wether kappa in K80, F84, or HKY85 is fixed or estimated">
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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174 <option value="0" selected="true">0 : estimated</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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175 <option value="1">1 : fixed (the next parameter below)</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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176 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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177
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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178 <param argument="kappa" type="float" value="2" label="Initial or fixed value of kappa" help="kappa refers to the transition/tranversion rate ratio"/>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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179
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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180 <param argument="fix_omega" type="select" label="Fixed or estimated omega" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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181 <option value="0" selected="true">0 : estimated</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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182 <option value="1">1 : fixed</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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183 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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184
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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185 <param argument="omega" type="float" value="0.2" label="Initial or fixed omega (according to your choice for fix_omega), for codons or codon-based AAs"/>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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186
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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187 <param argument="fix_alpha" type="select" label="Estimated or fixed gamma shape parameter" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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188 <option value="0">0 : estimate gamma shape parameter. Not recommended</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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189 <option value="1" selected="true">1 : fix it at alpha (the next parameter below)</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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190 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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191
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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192 <param argument="alpha" type="float" value="0" label="Initial or fixed value of alpha (gamma shape parameter)"
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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193 help="0: constant rate. fix_alpha !=1 and alpha !=0 are not compatible with NSsites !=0"/>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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194
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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195 <param argument="Malpha" type="select" label="Different alphas for genes" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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196 <option value="0">0 : one gamma distribution will be applied across all sites (one alpha)</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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197 <option value="1">1 : different gamma distribution is used for each gene or codon position (different alphas for genes)</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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198 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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199
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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200 <param argument="ncatG" type="integer" value="3" label="# of categories in dG of NSsites models" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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201
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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202 <param argument="fix_rho" type="select" label="Independence or correlation of rates at adjacent sites" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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203 <option value="0">0 : estimate rho</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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204 <option value="1" selected="true">1 : fix it at rho (the next parameter below)</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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205 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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206
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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207 <param argument="rho" type="float" value="0" label="Initial or fixed rho" help="fix_rho=1 and rho=0 : independent rates" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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208
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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209 <param argument="getSE" type="select" label="Estimates of the standard errors of estimated parameters." >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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210 <option value="0" selected="true">0 : don't want them</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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211 <option value="1">1 : want S.E.s of estimates</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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212 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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213
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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214 <param argument="RateAncestor" type="select" label="RateAncestor ; set 1 to force the program to do two additional analyses" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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215 <option value="0" selected="true">0 : usually use 0</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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216 <option value="1">1 : model of variable rates across site + empirical Bayesian reconstruction of ancestral sequences</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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217 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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218
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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219 <param argument="Small_Diff" type="float" value=".5e-6" label="Value used in the difference approximation of derivatives"/>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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220
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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221 <param argument="cleandata" type="select" label="Remove sites with ambiguity data" help="Warning : choosing 'yes' may remove a lot (possibly all) of data.">
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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222 <option value="0" selected="true">0 : no (don't remove ambiguous data)</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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223 <option value="1">1 : yes (remove ambiguous data)</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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224 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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225
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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226 <param argument="fix_blength" type="select" label="branch length dealing" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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227 <option value="0" selected="true">0 : ignore branch lengths</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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228 <option value="-1">-1 : start from random starting points</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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229 <option value="1">1 : initial values as written in the tree file</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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230 <option value="2">2 : fixed at values in the tree file</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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231 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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232
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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233 <param argument="method" type="select" label="Controls the iteration algorithm for estimating branch lengths" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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234 <option value="0" selected="true">0 : simultaneous (old paml algorithm)</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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235 <option value="1">1 : one branch at a time (newly implemented in paml ; does not work with clock=1,2,3)</option>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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236 </param>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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237 </section>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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238 </inputs>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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239
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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240 <outputs>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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241 <data format="txt" name="ctl" label="${tool.name} on ${on_string}: codeml.ctl" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
242 <data format="txt" name="2ngdn" from_work_dir="2NG.dN" label="${tool.name} on ${on_string}: 2NG.dN" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
243 <filter>adv['seqtype']=="1"</filter>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
244 </data>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
245 <data format="txt" name="2ngds" from_work_dir="2NG.dS" label="${tool.name} on ${on_string}: 2NG.dS" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
246 <filter>adv['seqtype']=="1"</filter>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
247 </data>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
248 <data format="txt" name="2ngt" from_work_dir="2NG.t" label="${tool.name} on ${on_string}: 2NG.t" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
249 <filter>adv['seqtype']=="1"</filter>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
250 </data>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
251 <data format="txt" name="lnf" from_work_dir="lnf" label="${tool.name} on ${on_string}: lnf"/>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
252 <data format="txt" name="rst" from_work_dir="rst" label="${tool.name} on ${on_string}: rst"/>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
253 <data format="txt" name="rst1" from_work_dir="rst1" label="${tool.name} on ${on_string}: rst1"/>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
254 <data format="txt" name="rub" from_work_dir="rub" label="${tool.name} on ${on_string}: rub"/>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
255 <data format="txt" name="run" from_work_dir="run_codeml" label="${tool.name} on ${on_string}: run_codeml"/>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
256 <data format="txt" name="4fold" from_work_dir="4fold.nuc" label="${tool.name} on ${on_string}: 4fold.nuc">
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
257 <filter>adv['verbose']=="1"</filter>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
258 </data>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
259 </outputs>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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260
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
261 <tests>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
262 <test>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
263 <conditional name="compat_model" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
264 <param name="brmodel" value="0" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
265 <param name="NSsites" value="0" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
266 </conditional>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
267 <param name="adv.fix_omega" value="0" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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268 <param name="adv.omega" value="0.2" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
269 <param name="RateAncestor" value="1" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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270 <param name="concat_nuc" ftype="fasta" value="concat.fasta" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
271 <param name="tree" ftype="txt" value="RAxML_bestTree" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
272 <output name="2ngdn" value="1_2ngdn" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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273 <output name="2ngds" value="1_2ngds" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
274 <output name="2ngt" value="1_2ngt" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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275 <output name="run" value="1_run_codeml" lines_diff="20"/>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
276 <output name="ctl" value="1_codeml.ctl" lines_diff="4" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
277 </test>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
278 <test>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
279 <conditional name="compat_model" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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280 <param name="brmodel" value="2" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
281 <param name="NSsites" value="0" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
282 </conditional>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
283 <param name="adv.fix_omega" value="0" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
284 <param name="adv.omega" value="0.2" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
285 <param name="RateAncestor" value="1" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
286 <param name="concat_nuc" ftype="fasta" value="concat.fasta" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
287 <param name="tree" ftype="txt" value="tree_model2" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
288 <output name="2ngdn" value="2_2ngdn" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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289 <output name="2ngds" value="2_2ngds" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
290 <output name="2ngt" value="2_2ngt" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
291 <output name="run" value="2_run_codeml" lines_diff="20" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
292 <output name="ctl" value="2_codeml.ctl" lines_diff="4" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
293 </test>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
294 <test>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
295 <conditional name="compat_model" >
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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296 <param name="brmodel" value="3" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
297 <param name="NSsites" value="2" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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298 </conditional>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
299 <param name="adv.fix_omega" value="0" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
300 <param name="adv.omega" value="0.2" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
301 <param name="RateAncestor" value="1" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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302 <param name="concat_nuc" ftype="fasta" value="concat.fasta" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
303 <param name="tree" ftype="txt" value="tree_model3" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
304 <output name="2ngdn" value="3_2ngdn" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
305 <output name="2ngds" value="3_2ngds" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
306 <output name="2ngt" value="3_2ngt" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
307 <output name="run" value="3_run_codeml" lines_diff="20"/>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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308 <output name="ctl" value="3_codeml.ctl" lines_diff="4" />
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
309 </test>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
310 </tests>
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
311
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
312 <help><![CDATA[
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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313 .. class:: infomark
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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314
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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diff changeset
315 **Galaxy integration** Victor Mataigne and ABIMS TEAM.
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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316
1
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0
iuc
parents: 0
diff changeset
317 Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool.
0
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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318
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
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319 ----------
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
diff changeset
320
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
iuc
parents:
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321 **CompCodeML (from paml package)**
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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322
1
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323 A few help is detailed below ; full and detailed codeml readme can be found on the paml website_.
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324
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325 .. _website: http://abacus.gene.ucl.ac.uk/software/paml.html
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326
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327 .. class:: warningmark
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328
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329 Due to their high number, some parameters incompatibility can remain.
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330
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331 This Galaxy implementation :
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332
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333 - handles incompatibilities between branch and sites models (the tool CANNOT be run with incompatible models).
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334 - warns the user in a help section when an advanced parameter has known incompatibilities (the tool CAN be run, but the output files will be empty).
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335
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336 We recommand to have a look at the full paml manual before looking at the advanced parameters, in order to spot parameters incompatibilities and to know what each model does. If you choose by mistake incompatible parameters, the output files will be empty, except the log file ("run_codeml" output) which will normally explicit the error.
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337
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338 .. class:: infomark
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339
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340 Known incompatibilities:
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341
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342 - 'seqtype' = 3 : only compatible with 'FSsites' = 0.
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343 - 'clock' = 2 : needs branch labels in the tree.
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344 - fix_alpha !=1 combined with alpha !=0 are not compatible with NSsites !=0
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345 - 'aaDist' = 0 is the only one compatible with 'NSsites' different than 0 and 'seqtype' = 1.
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346 - 'method' = 1 : does not work with 'clock' different than 0.
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347
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348 ----------
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349
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350 **Description**
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351
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352 .. class:: infomark
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353
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354 codeML finds positive selection within branches or codons within a tree and a set of sequences.
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355
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356 ----------
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357
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358 **Input files**
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359
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360 - a treefile in Newick format (with or without branch lengths).
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361 - a fasta file with sequences from the species of the tree file (one header/sequence per species) and run codeml (from the paml suite).
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362
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363 ----------
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364
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365 **Parameters**
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366
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367 Several models are available.
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368
0
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369 - branch models ("model" parameter).
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370 - sites models ("NSsites" parameter, model is left at 0).
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371 - branch-sites models (when model = 2 NSsites=2,3).
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372 - Clade models (when model=3 NSsites=2,3).
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373
0
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374 Basically, this tool write a configfile called codeml.ctl with the specified parameters and then launches codeml.
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375
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376 .. class:: infomark
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377
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378 Branch models allow the omega ratio to vary among branches in the phylogeny and are useful for detecting positive selection acting on particular lineages. Sites models allow the omega ratio to vary among sites (codons or amino acids).
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379
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380 Two pairs of models appear to be particularly useful, forming two likelihood ratio tests of positive selection. The first compares M1a ('NearlyNeutral', NSsites=1) and M2a ('PositiveSelection', NSsites=2), while the second compares M7 ('beta', NSsites=7) and M8 ('beta&ω', NSsites=8).
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381
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382 **Other examples of model**
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383
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384 How to run the branch-site models (A &amp; B in Yang &amp; Nielsen 2002 MBE) ?
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385 The options are :
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386
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387 - Model A: (model=2, NSsites=2).
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388 - Model B: (model=2, NSsites=3).
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389
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390 How to run the M0 (one-ratio) model :
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391
0
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392 model = 0, NSsites= = 0.
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393
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394 ----------
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395
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396 **Advanced Parameters**
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397
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398 .. class:: infomark
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399
1
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400 See paml complete manual and FAQ on the paml website_.
0
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401
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402 .. _website: http://abacus.gene.ucl.ac.uk/software/paml.html
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403
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404 **Details of some parameters :**
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405
1
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406 - 'kappa' denotes the transition/transversion rate ratio.
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407 - 'fix_kappa' specifies whether kappa in K80, F84, or HKY85 is given at a fixed value or is to be estimated by iteration from the data.
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408
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409 -> If fix_kappa = 1 (fixed), the value of kappa is the given value
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410
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411 -> If fix_kappa = 0 (estimated) the value of kappa is used as the initial estimate for iteration.
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412
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413 - 'alpha' refers to the shape parameter alpha of the gamma distribution for variable substitution rates across sites (Yang 1994a).
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414 - 'fix_alpha' works in a similar way that fix_kappa.
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415
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416 -> The model of a single rate for all sites is specified as fix_alpha = 1 and alpha = 0 (0 means infinity)
0
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417
1
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418 -> The (discrete-) gamma model is specified by a positive value for alpha, and 'ncatG' is then the number of categories for the discrete-gamma model. Values such as 5, 4, 8, or 10 are reasonable.
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419
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420 - fix_rho and rho work in a similar way and concern independence or correlation of rates at adjacent sites, where rho is the correlation parameter of the auto-discrete-gamma model (Yang 1995).
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0
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421
5750c1f4b0eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0
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422 -> The model of independent rates for sites is specified as fix_rho = 1 and rho = 0; choosing alpha = 0 further means a constant rate for all sites.
0
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423
1
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424 -> The auto-discrete-gamma model is specified by positive values for both alpha and rho.
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425
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426 -> The model of a constant rate for sites is a special case of the (discrete) gamma model with alpha = 0 (means infinity).
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427
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428 -> The model of independent rates for sites is a special case of the auto-discrete-gamma model with rho = 0.
0
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429
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430 ----------
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431
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432 **Output files**
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433
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434 - codeml.ctl : a copy of the control file (list of all the parameters used for the codeml run).
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435 - run_codeml : main result file name.
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436 - The 2NG.dN and 2NG.dS files are the Nei an Gojobori (1986) dN and dS values;
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437 - lnf, rst and rst1: Supplemental results.
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438 - rub : records of the iteration progress (i.e. the minimization of the negative log-likelihood).
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439
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440 ----------
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441
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442 **How to edit manually the tree file : Branch or node labels**
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443
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444 Some models implemented in codeml allow several groups of branches on the tree, which are assigned different parameters of interest.
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445
1
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446 - For example, in the local clock models (clock = 2 or 3), you can have, say, 3 branch rate groups, with low, medium, and high rates respectively.
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447 - Also the branch-specific codon models (model = 2 or 3 or codonml) allow different branch groups to have different ωs, leading to so called “two-ratios” and “three-ratios” models.
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448 - All those models require branches or nodes in the tree to be labeled. Branch labels are specified in the same way as branch lengths except that the symbol “#” is used rather than “:”. The branch labels are consecutive integers starting from 0, which is the default and does not have to be specified.
0
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449
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450 In ((Hsa_Human, Hla_gibbon) #1, ((Cgu/Can_colobus, Pne_langur), Mmu_rhesus), (Ssc_squirrelM, Cja_marmoset)); :
6c12b9745b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
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451 The internal branch ancestral to human and gibbon has the ratio ω1, while all other branches (with the default label #0) have the background ratio ω0.
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452
1
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453 The following trees are equivalent:
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454 - ((rabbit, rat) $1, human), goat_cow, marsupial);
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455 - (((rabbit #1, rat #1) #1, human), goat_cow, marsupial);
0
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456
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457 $ is the symbol for clade labels.
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458
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459 Rules concerning nested clade labels : The symbol # takes precedence over the symbol $, and clade labels close to the tips take precedence over clade labels for ancestral nodes close to the root.
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460
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461 In the tree ((((rabbit, rat) $2, human #3), goat_cow) $1, marsupial); :
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462 $1 is first applied to the whole clade of placental mammals (except for the human lineage), and then $2 is applied to the rabbit-rat clade.
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463 Equivalent tree with only '#' :
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464 ((((rabbit #2, rat #2) #2, human #3) #1, goat_cow #1) #1, marsupial);
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465 ]]></help>
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466
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467 <citations>
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468 <citation type="doi">10.1093/molbev/msm088</citation>
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469 </citations>
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470 </tool>