Mercurial > repos > iuc > pal2nal
comparison test-data/inputs/for_paml/test.cnt @ 0:a2a40f3bfbbd draft default tip
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 |
| parents | |
| children |
comparison
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| -1:000000000000 | 0:a2a40f3bfbbd |
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| 1 seqfile = test.codon | |
| 2 treefile = test.tree | |
| 3 outfile = test.codeml | |
| 4 | |
| 5 noisy = 0 * 0,1,2,3,9: how much rubbish on the screen | |
| 6 verbose = 0 * 1: detailed output, 0: concise output | |
| 7 runmode = -2 * 0: user tree; 1: semi-automatic; 2: automatic | |
| 8 * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise | |
| 9 | |
| 10 cleandata = 1 * "I added on 07/07/2004" Mikita Suyama | |
| 11 | |
| 12 seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs | |
| 13 CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table | |
| 14 model = 2 | |
| 15 * models for codons: | |
| 16 * 0:one, 1:b, 2:2 or more dN/dS ratios for branches | |
| 17 | |
| 18 NSsites = 0 * dN/dS among sites. 0:no variation, 1:neutral, 2:positive | |
| 19 icode = 0 * 0:standard genetic code; 1:mammalian mt; 2-10:see below | |
| 20 Mgene = 0 * 0:rates, 1:separate; 2:pi, 3:kappa, 4:all | |
| 21 | |
| 22 fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated | |
| 23 kappa = 2 * initial or fixed kappa | |
| 24 fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate | |
| 25 omega = 1 * initial or fixed omega, for codons or codon-transltd AAs | |
| 26 | |
| 27 fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha | |
| 28 alpha = .0 * initial or fixed alpha, 0:infinity (constant rate) | |
| 29 Malpha = 0 * different alphas for genes | |
| 30 ncatG = 4 * # of categories in the dG or AdG models of rates | |
| 31 | |
| 32 clock = 0 * 0: no clock, unrooted tree, 1: clock, rooted tree | |
| 33 getSE = 0 * 0: don't want them, 1: want S.E.s of estimates | |
| 34 RateAncestor = 0 * (1/0): rates (alpha>0) or ancestral states (alpha=0) | |
| 35 method = 0 * 0: simultaneous; 1: one branch at a time | |
| 36 |