Mercurial > repos > iuc > codeml

comparison test-data/2_codeml.ctl @ 0:961a712f9743 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
author iuc
date Tue, 29 Aug 2017 19:12:01 -0400
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children ba71e26d5bdc
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-1:000000000000 0:961a712f9743
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2 seqfile = /tmp/saskia/tmphfQhiQ/files/000/dataset_12.dat * sequence data file name
3 outfile = run_codeml * main result file name
4 treefile = /tmp/saskia/tmphfQhiQ/files/000/dataset_13.dat * tree structure file name
5 noisy = 9 * 0,1,2,3,9: how much rubbish on the screen
6 verbose = 0 * 1: detailed output, 0: concise output
7 runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic
8 * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise
9 seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs
10 CodonFreq = 1 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
11 clock = 0 * 0:no clock, 1:clock; 2:local clock
12 aaDist = 0 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
13 * 7:AAClasses
14 aaRatefile = wag.dat * only used for aa seqs with model=empirical(_F)
15 * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own
16 model = 2
17 * models for codons:
18 * 0:one, 1:b, 2:2 or more dN/dS ratios for branches
19 * models for AAs or codon-translated AAs:
20 * 0:poisson, 1:proportional,2:Empirical,3:Empirical+F
21 * 6:FromCodon, 8:REVaa_0, 9:REVaa(nr=189)
22 NSsites = 0 * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs;
23 * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ
24 * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1;
25 * 13:3normal>0
26 icode = 0 * 0:universal code; 1:mammalian mt; 2-11:see below
27 Mgene = 0 * 0:rates, 1:separate;
28 fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated
29 kappa = 2.0 * initial or fixed kappa
30 fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate
31 omega = 0.2 * initial or fixed omega, for codons or codon-based AAs
32 fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha
33 alpha = 0.0 * initial or fixed alpha, 0:infinity (constant rate)
34 Malpha = 0 * 1: different alphas for genes, 0 : one alpha
35 ncatG = 3 * # of categories in dG of NSsites models
36 fix_rho = 1 * 0: estimate rho; 1: fix it at rho
37 rho = 0.0 * initial or fixed rho, 0:no correlation
38 getSE = 0 * 0: don't want them, 1: want S.E.s of estimates
39 RateAncestor = 1 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
40 Small_Diff = 5e-07
41 cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
42 fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed
43 method = 0 * 0: simultaneous; 1: one branch at a time
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