PAML! Oh, good fun.

The worst part about PAML is getting ready to run PAML.

Be sure to keep organized. To run PAML, navigate to /Applications/paml4.8/bin/. There should be all the different PAML binaries listed.


For the null model:

bash-3.2$ sudo ./codeml codeml.ctl 

Tree file with two groups: group 0 is taxa with 

(((((((((((((((((((((Artibeus_fimbriatus,(Artibeus_jamaicensis,Artibeus_obscurus)),Artibeus_inopinatus),Artibeus_concolor),((((Artibeus_watsoni,Artibeus_incomitatus),Artibeus_phaeotis),Artibeus_cinereus),(Artibeus_glaucus,Artibeus_gnomus))),((Phyllops_falcatus,(Ariteus_flavescens,Ardops_nichollsi)),((Pygoderma_bilabiatum,Sphaeronycteris_toxophyllum),Centurio_senex))),Ectophylla_alba),Enchisthenes_hartii),((((((((Platyrrhinus_nigellus,Platyrrhinus_dorsalis),(Platyrrhinus_infuscus,Platyrrhinus_aurarius)),Platyrrhinus_albericoi),Platyrrhinus_lineatus),Vampyrodes_caraccioli),(Vampyressa_thyone,Mesophylla_macconnelli)),(((Chiroderma_villosum,Chiroderma_improvisum),Chiroderma_doriae),(Vampyressa_brocki,Vampyressa_bidens))),Uroderma_magnirostrum)),(((Sturnira_bogotensis,Sturnira_tildae),Sturnira_magna),(Sturnira_oporaphilum,Sturnira_lilium))),Rhinophylla_fischerae),(((((Carollia_perspicillata,Carollia_brevicauda),Carollia_sowelli),Carollia_subrufa),Carollia_castanea),(Glyphonycteris_sylvestris,Trinycteris_nicefori))),((((Lonchophylla_hesperia,Lionycteris_spurrelli),Platalina_genovensium),Lonchophylla_chocoana),Lonchophylla_mordax)),((((((Glossophaga_longirostris,Glossophaga_commissarisi),Glossophaga_soricina),Leptonycteris_curasoae),((Phyllonycteris_poeyi,(Erophylla_sezekorni,Erophylla_bombifrons)),(Brachyphylla_pumila,Brachyphylla_cavernarum))$1),((Musonycteris_harrisoni,Choeroniscus_godmani),((Anoura_latidens,Anoura_geoffroyi),Anoura_caudifer))),(Lonchorhina_aurita,Lonchorhina_inusitata))),(((Phyllostomus_discolor,(Lophostoma_brasiliense,(Lophostoma_evotis,Lophostoma_silvicola))),(Tonatia_saurophila,Tonatia_bidens)),Mimon_cozumelae)),((Diaemus_youngi,Desmodus_rotundus),Diphylla_ecaudata)),((Micronycteris_hirsuta,(Micronycteris_minuta,Micronycteris_schmidtorum)),Lampronycteris_brachyotis)),(((Pteronotus_davyi,Pteronotus_quadridens),Pteronotus_parnellii),(Mormoops_megalophylla,Mormoops_blainvillei)$1)),(Noctilio_leporinus,Furipterus_horrens)$1),(Thyroptera_lavali,Thyroptera_tricolor)$1),Tadarida_brasilense#1,Chilonatalus_micropus#1),Cormura_brevirostris#1,((Megaderma_lyra,(Rhinolophus_ferrumequinum,Hipposideros_pratti)),((Acerodon_celebensis,Eonycteris_spelaea),Cynopterus_sphinx))$1);

codeml.CladeC.ctl
      seqfile = bat_data_match.phylip * sequence data filename
     treefile = bat_tree_match_cladeModelC_2groups.tre      * tree structure file name
      outfile = trpc2cladeModelC_2groups_0point1.txt           * main result file name

        noisy = 9  * 0,1,2,3,9: how much rubbish on the screen
      verbose = 0  * 0: concise; 1: detailed, 2: too much
      runmode = 0  * 0: user tree

      seqtype = 1  * 1:codons; 2:AAs; 3:codons-->AAs
    CodonFreq = 2  * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
        clock = 0  * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis

  * Model C: model = 3  NSsites = 2 
    * Model D: model = 3  NSsites = 3

        model = 3  * 3 = clade models
      NSsites = 2  * choose "2" or "3"
 
        icode = 0  * 0:universal code; 1:mammalian mt; 2-10:see below

    fix_kappa = 0  * 1: kappa fixed, 0: kappa to be estimated
        kappa = 2.5  * initial or fixed kappa

    fix_omega = 0  * 1: omega or omega_1 fixed, 0: estimate 
        omega = 0.1 * 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)

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

        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 = .2e-6
    cleandata = 0  * remove sites with ambiguity data (1:yes, 0:no)?

We are ready to go. Run the control file.

bash-3.2$ sudo ./codeml codeml.CladeC.ctl