Pairwise AAML

[Yuma]

Hi all,

   I'm trying to run a pairwise AAML, but I'm getting "tree file not found." I was under the impression that trees were not required for pairwise analyses. Is this different for amino acid files? Any suggestions?

Amino Acid file:

>XP

ME------ETIAKMKPAQKPTELKKPPKPYPFNFVSRQEWGALEPTGKIEPIDHPIEYFG

YKFSNTDPCISRTACLKNIKELQKYHMFAKDLPDIAYNFIVGGDLSIYEGRGWFLKPTYL

DDKLREYDGKYLSIGYMGLEGAGIDRNFYCIEILDIRDDLILYGIEHGYLDENARYDRID

VWNQ

>RA

MSTYTDGMSGMSGLRPATMPKLERPPPKPYNFSFVSRLEWGAVEATEKLPLLDHPIDYFI

YKFSETDPCISKRACLKNIKDLQKYHMLVKGLPDIAYNFIIGGDLRVYEGRGWFYKPTLL

DDKQREYDGKLLSIGYMGLKGAGLDRNFYCVEILDLREDLIDYGIEQGYMDDNCKIDRID

VWDQ

CTL file:

seqfile = OG0007841.fa.aligned * sequence data file name

outfile = mlc * main result file name

*treefile =

noisy = 9 * 0,1,2,3,9: how much rubbish on the screen

verbose = 0 * 1: detailed output, 0: concise output

runmode = -2 * 0: user tree; 1: semi-automatic; 2: automatic

             * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise

seqtype = 2 * 1:codons; 2:AAs; 3:codons-->AAs

CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table

              * ndata = 10

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 = 0

        * 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

                 * 5:FromCodon0, 6:FromCodon1, 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 * initial or fixed kappa

fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate

omega = .4 * 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. * initial or fixed alpha, 0:infinity (constant rate)

Malpha = 0 * different alphas for genes

ncatG = 3 * # of categories in dG of NSsites models

fix_rho = 1 * 0: estimate rho; 1: fix it at rho

rho = 0. * initial or fixed rho, 0:no correlation

getSE = 0 * 0: don't want them, 1: want S.E.s of estimates

RateAncestor = 0 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)

Small_Diff = .5e-6

* cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?

* fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed, 3: proportional

method = 0 * 0: simultaneous; 1: one branch at a time

[Sishuo Wang]

Hi Yuma, 

I guess you still need a tree, unless you use yn00 but yn00 is not for amino acid sequence. See also aaml.ctl, stewart.aa, and stewart.trees under the folder example/.

Best,

Sishuo