Skip to content

Commit

Permalink
updated precooked runs
Browse files Browse the repository at this point in the history
  • Loading branch information
bjoelle committed Aug 11, 2023
1 parent 859370f commit 55d5858
Show file tree
Hide file tree
Showing 4 changed files with 18,042 additions and 7,206 deletions.
36 changes: 36 additions & 0 deletions precooked_runs/primates.MCC.tre
@@ -0,0 +1,36 @@
#NEXUS

Begin taxa;
Dimensions ntax=12;
Taxlabels
Gorilla
Homo_sapiens
Hylobates
Lemur_catta
M._fascicularis
M._mulatta
M._sylvanus
Macaca_fuscata
Pan
Pongo
Saimiri_sciureus
Tarsius_syrichta
;
End;
Begin trees;
Translate
1 Gorilla,
2 Homo_sapiens,
3 Hylobates,
4 Lemur_catta,
5 M._fascicularis,
6 M._mulatta,
7 M._sylvanus,
8 Macaca_fuscata,
9 Pan,
10 Pongo,
11 Saimiri_sciureus,
12 Tarsius_syrichta
;
tree TREE1 = ((((((1[&height=6.24767163881636E-15,height_95%_HPD={0.0,1.4210854715202004E-14},height_median=0.0,height_range={0.0,4.263256414560601E-14},lambda=0.08344980749258432,lambda_95%_HPD={0.005899731346275409,0.2027371483655237},lambda_median=0.06575436144812986,lambda_range={0.0012561595112014182,1.6236341053763161},length=8.500343662987042,length_95%_HPD={6.145036731212613,10.891969265157144},length_median=8.392517980137399,length_range={4.478851757752587,14.279472508243089},mu=0.03187313504876394,mu_95%_HPD={1.9188579100884963E-4,0.09238596830123363},mu_median=0.020725338824577656,mu_range={1.9188579100884963E-4,1.1002474190251723}]:8.500343662987044,(2[&height=6.289770079002109E-15,height_95%_HPD={0.0,2.8421709430404007E-14},height_median=0.0,height_range={0.0,4.263256414560601E-14},lambda=0.09510770411173586,lambda_95%_HPD={0.0038827504390146444,0.25365622838404345},lambda_median=0.06890836417811519,lambda_range={6.393168653161898E-4,1.7083731712654915},length=5.966052876889702,length_95%_HPD={4.995416387831341,6.8992820820523235},length_median=5.976385420850207,length_range={3.9576001566866594,7.516322103937895},mu=0.03541806136313477,mu_95%_HPD={1.9945268475715154E-4,0.10689235374437311},mu_median=0.02137425303813721,mu_range={1.9945268475715154E-4,0.8388342986851057}]:5.966052876889702,9[&height=6.289770079002109E-15,height_95%_HPD={0.0,2.8421709430404007E-14},height_median=0.0,height_range={0.0,4.263256414560601E-14},lambda=0.09473983704381694,lambda_95%_HPD={0.004300293877402622,0.2537834367402214},lambda_median=0.06915049586890933,lambda_range={0.0010702055300305688,1.9571587286511118},length=5.966052876889702,length_95%_HPD={4.995416387831341,6.8992820820523235},length_median=5.976385420850207,length_range={3.9576001566866594,7.516322103937895},mu=0.03510756109227353,mu_95%_HPD={3.648254724039416E-4,0.1051600418980704},mu_median=0.021528290632234937,mu_range={2.733140080088641E-4,1.2932830131679562}]:5.966052876889702)[&CAheight_95%_HPD={4.995416387831341,6.8992820820523235},CAheight_mean=5.966052876889708,CAheight_median=5.976385420850207,CAheight_range={3.9576001566866594,7.516322103937924},height=5.966052876889708,height_95%_HPD={4.995416387831341,6.8992820820523235},height_median=5.976385420850207,height_range={3.9576001566866594,7.516322103937924},lambda=0.08242031700907669,lambda_95%_HPD={0.008226021677903539,0.18118508562283836},lambda_median=0.06789296421178367,lambda_range={0.003420595684153565,2.6464894907646217},length=2.534290786097319,length_95%_HPD={0.7271774372638191,4.690550714277606},length_median=2.4146918300173894,length_range={0.06066608026804943,7.6047961377012},mu=0.032095890214460965,mu_95%_HPD={6.763852020177108E-4,0.08910924454893467},mu_median=0.020906679258785598,mu_range={6.763852020177108E-4,2.149098480453088},posterior=1.0]:2.534290786097343)[&CAheight_95%_HPD={6.145036731212613,10.891969265157158},CAheight_mean=8.500343662987051,CAheight_median=8.392517980137427,CAheight_range={4.478851757752594,14.279472508243117},height=8.500343662987051,height_95%_HPD={6.145036731212613,10.891969265157158},height_median=8.392517980137427,height_range={4.478851757752594,14.279472508243117},lambda=0.07678979216547284,lambda_95%_HPD={0.012931424784358719,0.1545872378508527},lambda_median=0.06348668311108914,lambda_range={0.006276774540610244,2.0992246885747115},length=11.658473052016921,length_95%_HPD={6.25050631365022,17.31387689825243},length_median=11.381945747496204,length_range={4.042890132555264,28.895682703178522},mu=0.031453442482639024,mu_95%_HPD={9.188489474226851E-4,0.08008634176597101},mu_median=0.02003025586795891,mu_range={6.466303128759411E-4,2.0263361021334463},posterior=1.0]:11.658882566913936,10[&height=6.183208402281931E-15,height_95%_HPD={0.0,1.4210854715202004E-14},height_median=0.0,height_range={0.0,2.8421709430404007E-14},lambda=0.07213823351861576,lambda_95%_HPD={0.007922537618333007,0.1679188416656928},lambda_median=0.05935149980776403,lambda_range={6.732788799920745E-4,2.0814273603158595},length=20.159018048025327,length_95%_HPD={13.506588764071218,27.302741517775033},length_median=19.850545849523975,length_range={9.595123251485035,38.246834523327635},mu=0.028212269004413065,mu_95%_HPD={2.8230685657532463E-4,0.08017421976741777},mu_median=0.01889578284518282,mu_range={2.985669469094189E-5,1.5022858960600336}]:20.15922622990098)[&CAheight_95%_HPD={13.506588764071225,27.302741517775033},CAheight_mean=20.159226229900987,CAheight_median=19.85054584952399,CAheight_range={9.595123251485042,38.246834523327635},height=20.15473636874097,height_95%_HPD={13.544071973222728,27.315101065698812},height_median=19.84737086022823,height_range={9.595123251485042,38.246834523327635},lambda=0.06622871144478402,lambda_95%_HPD={0.018126318965978026,0.13151042469791407},lambda_median=0.0582009766236011,lambda_range={0.010187372211466098,2.292413563919757},length=6.817715664887058,length_95%_HPD={2.126135320968686,12.060483643321504},length_median=6.519543904157011,length_range={0.44270860706862436,21.971387381076113},mu=0.0271794731717367,mu_95%_HPD={0.0010720117182437896,0.07360543705033384},mu_median=0.01868872520362612,mu_range={6.08509757281297E-4,1.0284713546043338},posterior=0.998703943714127]:6.808879521644187,3[&height=6.223991266211876E-15,height_95%_HPD={0.0,1.4210854715202004E-14},height_median=0.0,height_range={0.0,2.8421709430404007E-14},lambda=0.06473313324957972,lambda_95%_HPD={0.005948144373985505,0.1433137235631477},lambda_median=0.05481704148983402,lambda_range={5.578433182402743E-4,0.7152353275028511},length=26.96748805477251,length_95%_HPD={18.13366959998592,36.12780702809951},length_median=26.579365361273105,length_range={12.126058764222662,51.6177426332369},mu=0.025849854930746093,mu_95%_HPD={2.7318473439926587E-5,0.07374278874409525},mu_median=0.017777547184380068,mu_range={2.7318473439926587E-5,0.5541164351883263}]:26.968105751545167)[&CAheight_95%_HPD={18.13366959998592,36.12780702809954},CAheight_mean=26.968105751545174,CAheight_median=26.57936536127312,CAheight_range={12.12605876422267,51.61774263323693},height=26.968105751545174,height_95%_HPD={18.13366959998592,36.12780702809954},height_median=26.57936536127312,height_range={12.12605876422267,51.61774263323693},lambda=0.06216234202033768,lambda_95%_HPD={0.018548675693566354,0.11888058056885424},lambda_median=0.054529479318950795,lambda_range={0.00980860186531995,0.683649640520635},length=22.095021155091988,length_95%_HPD={11.912936122159564,33.17322084577333},length_median=21.509998310383743,length_range={7.60188397494905,49.66785870008698},mu=0.026292109509542992,mu_95%_HPD={9.054214732242523E-4,0.0757960468973287},mu_median=0.01789544754821192,mu_range={6.083504659874389E-4,0.5825360419426442},posterior=1.0]:22.095021155092162,((5[&height=6.2805610452114765E-15,height_95%_HPD={0.0,1.4210854715202004E-14},height_median=0.0,height_range={0.0,5.6843418860808015E-14},lambda=0.08676092290657855,lambda_95%_HPD={0.007159538025165653,0.23076330152978278},lambda_median=0.06447438417894917,lambda_range={4.5227220476608347E-4,1.3398514742015175},length=6.0591886736968394,length_95%_HPD={3.913276613692773,8.490228276975614},length_median=5.956546454196541,length_range={2.7123002458475014,12.020637252778243},mu=0.03315687311096038,mu_95%_HPD={3.850520437621622E-4,0.09975365221804584},mu_median=0.021199334621673668,mu_range={1.0642635956362863E-4,0.583011638380188}]:6.059188673696841,(6[&height=6.1884707073051494E-15,height_95%_HPD={0.0,2.8421709430404007E-14},height_median=0.0,height_range={0.0,5.6843418860808015E-14},lambda=0.10114108803232146,lambda_95%_HPD={0.004491645595875592,0.28551261366240993},lambda_median=0.06740735762245124,lambda_range={0.0014883928379249114,3.265465277071241},length=2.020840697725104,length_95%_HPD={1.195247810569569,3.0353650862339947},length_median=1.961695924228934,length_range={0.7947230724444978,5.049557709448067},mu=0.03721141769308055,mu_95%_HPD={4.197546382613269E-4,0.12419699509733244},mu_median=0.021909032200198086,mu_range={3.234474225607074E-4,0.6864297235752668}]:2.020840697725104,8[&height=6.1884707073051494E-15,height_95%_HPD={0.0,2.8421709430404007E-14},height_median=0.0,height_range={0.0,5.6843418860808015E-14},lambda=0.10006117671309338,lambda_95%_HPD={0.0028629013731559945,0.28052709637100465},lambda_median=0.06820736496199628,lambda_range={0.0010224699747547336,5.056729965067403},length=2.020840697725104,length_95%_HPD={1.195247810569569,3.0353650862339947},length_median=1.961695924228934,length_range={0.7947230724444978,5.049557709448067},mu=0.03699982557376752,mu_95%_HPD={3.668445312675261E-4,0.12036300694170242},mu_median=0.02179096180831252,mu_range={7.577309715684634E-5,1.59499413175007}]:2.020840697725104)[&CAheight_95%_HPD={1.1952478105695832,3.0353650862339947},CAheight_mean=2.0208406977251103,CAheight_median=1.961695924228934,CAheight_range={0.7947230724445049,5.049557709448095},height=2.0208406977251103,height_95%_HPD={1.1952478105695832,3.0353650862339947},height_median=1.961695924228934,height_range={0.7947230724445049,5.049557709448095},lambda=0.09132587143947785,lambda_95%_HPD={0.009362662773635724,0.23701026303837944},lambda_median=0.06613175889408872,lambda_range={0.006674781067930029,1.8913651465393593},length=4.03834797597174,length_95%_HPD={2.225953473032959,5.966558519762387},length_median=3.9606763962874965,length_range={1.5275163099949864,8.889451573654156},mu=0.03474023586704382,mu_95%_HPD={4.8370141918146537E-4,0.10898549185999737},mu_median=0.02164497910348197,mu_range={4.8370141918146537E-4,0.7232397732109265},posterior=1.0]:4.038347975971737)[&CAheight_95%_HPD={3.913276613692773,8.490228276975614},CAheight_mean=6.059188673696847,CAheight_median=5.956546454196541,CAheight_range={2.7123002458475014,12.020637252778243},height=6.059188673696847,height_95%_HPD={3.913276613692773,8.490228276975614},height_median=5.956546454196541,height_range={2.7123002458475014,12.020637252778243},lambda=0.07947323280003987,lambda_95%_HPD={0.014689041730341244,0.18049535393454177},lambda_median=0.06413327424634428,lambda_range={0.009806653187891807,2.802216828374005},length=4.43372006950207,length_95%_HPD={1.8331233038821892,7.146901484932783},length_median=4.305070244493251,length_range={0.5272782822425981,12.26233218730323},mu=0.031574630076768744,mu_95%_HPD={6.403439648790565E-4,0.08971635519618616},mu_median=0.0209212427832087,mu_range={6.403439648790565E-4,2.2228363435334937},posterior=1.0]:4.433720069502029,7[&height=6.1963641648399776E-15,height_95%_HPD={0.0,1.4210854715202004E-14},height_median=0.0,height_range={0.0,4.263256414560601E-14},lambda=0.07478491883413727,lambda_95%_HPD={0.009813189557912855,0.18147963598740574},lambda_median=0.06007126914263597,lambda_range={0.0011454618374605737,1.306459474391834},length=10.492908743198871,length_95%_HPD={6.805976178643675,14.363075304261145},length_median=10.322413472828288,length_range={5.4536097678182855,22.088408107860943},mu=0.029441918113826206,mu_95%_HPD={2.7616953769894233E-4,0.08745977656949164},mu_median=0.019741200718023665,mu_range={6.233577679553278E-5,0.9638079122751875}]:10.492908743198871)[&CAheight_95%_HPD={6.805976178643675,14.363075304261173},CAheight_mean=10.492908743198877,CAheight_median=10.322413472828288,CAheight_range={5.453609767818293,22.08840810786097},height=10.492908743198877,height_95%_HPD={6.805976178643675,14.363075304261173},height_median=10.322413472828288,height_range={5.453609767818293,22.08840810786097},lambda=0.06863907189479636,lambda_95%_HPD={0.01812239740053739,0.137974814076444},lambda_median=0.059594015670501085,lambda_range={0.010523119984056577,0.5527748541617005},length=38.57021816343825,length_95%_HPD={25.71830760602642,54.511213352992414},length_median=37.81726286091265,length_range={18.228365739952196,76.46330971678111},mu=0.027886612488077125,mu_95%_HPD={5.628142434782899E-4,0.07706048596527028},mu_median=0.01963838786233369,mu_range={5.628142434782899E-4,0.3388229555121908},posterior=1.0]:38.57021816343846)[&CAheight_95%_HPD={32.67787843235055,66.55128850423961},CAheight_mean=49.063126906637336,CAheight_median=48.290307751111236,CAheight_range={24.185899572579466,94.73370252502252},height=49.063126906637336,height_95%_HPD={32.67787843235055,66.55128850423961},height_median=48.290307751111236,height_range={24.185899572579466,94.73370252502252},lambda=0.06218910764258782,lambda_95%_HPD={0.01509902231483551,0.1258314807704077},lambda_median=0.052643789463726776,lambda_range={0.010992566200447654,0.8278679648602315},length=18.82548646231436,length_95%_HPD={5.947061225423504,31.852211105553614},length_median=18.047845103245173,length_range={0.3037981514536199,55.141001842264714},mu=0.027299345069256766,mu_95%_HPD={6.699800721508923E-4,0.0825970373484355},mu_median=0.01695591836600924,mu_range={5.74117466795774E-4,0.5975199476674108},posterior=1.0]:18.829629503814388,11[&height=6.1976797410957824E-15,height_95%_HPD={0.0,1.4210854715202004E-14},height_median=0.0,height_range={0.0,2.8421709430404007E-14},lambda=0.04968114485135557,lambda_95%_HPD={0.0048326414180868416,0.10170052383977894},lambda_median=0.04357964387876302,lambda_range={2.1031792115127091E-4,2.2365673407604},length=67.89180820493769,length_95%_HPD={44.0234282704556,93.13100080051042},length_median=66.65868429933532,length_range={35.25055127875042,135.25286578412704},mu=0.020643039633437953,mu_95%_HPD={9.326592807903025E-6,0.06003342853046341},mu_median=0.013741239430913002,mu_range={9.326592807903025E-6,1.02971006558639}]:67.89275641045172)[&CAheight_95%_HPD={44.0234282704556,93.13100080051042},CAheight_mean=67.89275641045172,CAheight_median=66.65868429933532,CAheight_range={35.25055127875043,135.25286578412704},height=67.87095110179739,height_95%_HPD={44.09363841005738,93.13100080051042},height_median=66.64388854654298,height_range={35.25055127875043,135.25286578412704},lambda=0.06388484531834202,lambda_95%_HPD={0.010730934329503979,0.15795467756390685},lambda_median=0.048856019942313145,lambda_range={0.008933321381809814,2.1275353487347535},length=23.442196575275997,length_95%_HPD={8.796244297790658,40.349102007496455},length_median=22.803948711379455,length_range={0.9100508112816925,67.75351879973043},mu=0.0290644888994341,mu_95%_HPD={4.1476666288090827E-4,0.0985052271244137},mu_median=0.015451775113282983,mu_range={4.1476666288090827E-4,1.2051973991539011},posterior=0.998703943714127]:23.439009975989393,(4[&height=6.1976797410957824E-15,height_95%_HPD={0.0,1.4210854715202004E-14},height_median=0.0,height_range={0.0,2.8421709430404007E-14},lambda=0.04528367292722262,lambda_95%_HPD={0.005346863949863339,0.09661352467390115},lambda_median=0.04016449813683538,lambda_range={1.4981393530433105E-4,0.4143194982698057},length=68.35966549438574,length_95%_HPD={43.184514344724086,97.2760464595423},length_median=66.71484576351197,length_range={31.361918944129787,142.12462829001265},mu=0.018484722520484477,mu_95%_HPD={6.205653997554512E-5,0.05403818865577239},mu_median=0.012834314568266043,mu_range={2.620040726183532E-5,0.3259043928732391}]:68.38275624606982,12[&height=6.1976797410957824E-15,height_95%_HPD={0.0,1.4210854715202004E-14},height_median=0.0,height_range={0.0,2.8421709430404007E-14},lambda=0.04538268939255128,lambda_95%_HPD={0.003121294562463687,0.09496838869777514},lambda_median=0.040307207808108265,lambda_range={6.982509716884518E-4,0.3812977295602498},length=68.37865119081478,length_95%_HPD={43.04000741284351,97.30211385509234},length_median=66.71484576351197,length_range={31.361918944129787,154.1662114489125},mu=0.0185346948374044,mu_95%_HPD={2.1994817832065713E-4,0.05459793953828417},mu_median=0.012688213247945045,mu_range={6.402416184855399E-5,0.3523312825090415}]:68.38275624606982)[&CAheight_95%_HPD={43.04000741284351,97.30211385509234},CAheight_mean=68.38275624606982,CAheight_median=66.71484576351197,CAheight_range={31.361918944129787,154.1662114489125},height=68.19363112381312,height_95%_HPD={42.98378265336199,96.60985102618363},height_median=66.58664051398952,height_range={31.361918944129787,140.90578086150654},lambda=0.05426092979567195,lambda_95%_HPD={0.008104334311239848,0.12972027978210365},lambda_median=0.04322621349797803,lambda_range={0.004883492048668762,0.6306631936232879},length=23.10218231599954,length_95%_HPD={6.547797925682971,40.10831714334724},length_median=22.5169225492395,length_range={0.29140359275433525,65.9667227341391},mu=0.024382139794508158,mu_95%_HPD={3.9169486461663783E-4,0.08024100166730672},mu_median=0.013862382832430386,mu_range={3.9169486461663783E-4,0.5899407250413923},posterior=0.9931494167746714]:22.9490101403713)[&CAheight_95%_HPD={61.478684498460225,125.554496020528},CAheight_mean=91.33176638644112,CAheight_median=89.87458876233697,CAheight_range={45.75222276499472,182.5859850077485},height=91.33176638644112,height_95%_HPD={61.478684498460225,125.554496020528},height_median=89.87458876233697,height_range={45.75222276499472,182.5859850077485},lambda=0.11793457824160272,lambda_95%_HPD={0.006020283063210209,0.39116865647616494},lambda_median=0.04765797470090583,lambda_range={0.004461296230935997,20.205149735601786},length=0.0,mu=0.060293679896725134,mu_95%_HPD={3.367361946818385E-4,0.21338382128038744},mu_median=0.015083265948944644,mu_range={3.367361946818385E-4,14.290696528618874},posterior=1.0]:0.0;
End;

0 comments on commit 55d5858

Please sign in to comment.