Mercurial > repos > iuc > codeml
diff test-data/2_codeml.ctl @ 0:961a712f9743 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
author | iuc |
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date | Tue, 29 Aug 2017 19:12:01 -0400 |
parents | |
children | ba71e26d5bdc |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2_codeml.ctl Tue Aug 29 19:12:01 2017 -0400 @@ -0,0 +1,45 @@ + + seqfile = /tmp/saskia/tmphfQhiQ/files/000/dataset_12.dat * sequence data file name + outfile = run_codeml * main result file name + treefile = /tmp/saskia/tmphfQhiQ/files/000/dataset_13.dat * tree structure file name + noisy = 9 * 0,1,2,3,9: how much rubbish on the screen + verbose = 0 * 1: detailed output, 0: concise output + runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic + * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise + seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs + CodonFreq = 1 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table + clock = 0 * 0:no clock, 1:clock; 2:local clock + aaDist = 0 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a + * 7:AAClasses + aaRatefile = wag.dat * only used for aa seqs with model=empirical(_F) + * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own + model = 2 + * models for codons: + * 0:one, 1:b, 2:2 or more dN/dS ratios for branches + * models for AAs or codon-translated AAs: + * 0:poisson, 1:proportional,2:Empirical,3:Empirical+F + * 6:FromCodon, 8:REVaa_0, 9:REVaa(nr=189) + NSsites = 0 * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs; + * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ + * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1; + * 13:3normal>0 + icode = 0 * 0:universal code; 1:mammalian mt; 2-11:see below + Mgene = 0 * 0:rates, 1:separate; + fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated + kappa = 2.0 * initial or fixed kappa + fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate + omega = 0.2 * initial or fixed omega, for codons or codon-based AAs + fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha + alpha = 0.0 * initial or fixed alpha, 0:infinity (constant rate) + Malpha = 0 * 1: different alphas for genes, 0 : one alpha + ncatG = 3 * # of categories in dG of NSsites models + fix_rho = 1 * 0: estimate rho; 1: fix it at rho + rho = 0.0 * initial or fixed rho, 0:no correlation + getSE = 0 * 0: don't want them, 1: want S.E.s of estimates + RateAncestor = 1 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2) + Small_Diff = 5e-07 + cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)? + fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed + method = 0 * 0: simultaneous; 1: one branch at a time + + \ No newline at end of file