Mercurial > repos > iuc > pal2nal

annotate test-data/inputs/for_paml/test.cnt @ 0:a2a40f3bfbbd draft default tip

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planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
author iuc
date Sun, 09 Nov 2025 10:56:06 +0000
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a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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1 seqfile = test.codon
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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2 treefile = test.tree
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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3 outfile = test.codeml
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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5 noisy = 0 * 0,1,2,3,9: how much rubbish on the screen
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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6 verbose = 0 * 1: detailed output, 0: concise output
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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7 runmode = -2 * 0: user tree; 1: semi-automatic; 2: automatic
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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8 * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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10 cleandata = 1 * "I added on 07/07/2004" Mikita Suyama
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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12 seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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13 CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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14 model = 2
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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15 * models for codons:
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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16 * 0:one, 1:b, 2:2 or more dN/dS ratios for branches
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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18 NSsites = 0 * dN/dS among sites. 0:no variation, 1:neutral, 2:positive
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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19 icode = 0 * 0:standard genetic code; 1:mammalian mt; 2-10:see below
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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20 Mgene = 0 * 0:rates, 1:separate; 2:pi, 3:kappa, 4:all
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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22 fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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23 kappa = 2 * initial or fixed kappa
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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24 fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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25 omega = 1 * initial or fixed omega, for codons or codon-transltd AAs
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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27 fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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28 alpha = .0 * initial or fixed alpha, 0:infinity (constant rate)
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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29 Malpha = 0 * different alphas for genes
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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30 ncatG = 4 * # of categories in the dG or AdG models of rates
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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32 clock = 0 * 0: no clock, unrooted tree, 1: clock, rooted tree
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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33 getSE = 0 * 0: don't want them, 1: want S.E.s of estimates
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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34 RateAncestor = 0 * (1/0): rates (alpha>0) or ancestral states (alpha=0)
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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35 method = 0 * 0: simultaneous; 1: one branch at a time
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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