Want a MrBayes Block as an example

Ashok Kumar Mallik

unread,

Aug 3, 2017, 4:56:00 AM8/3/17

to CIPRES Science Gateway Users

Hi All,

If any user has successfully run MrBayes in CIPRES then kindly send me a format for working "MrBayes Block"?

I want to see it as an example to run in CIPRES.

Please email to my email id asho...@gmail.com

Thanks in advance

Ashok

Mark Miller

unread,

Aug 3, 2017, 9:31:57 AM8/3/17

to CIPRES Science Gateway Users

Hi Ashok,

Here is a simple one, I will send you a complex one privately.

begin mrbayes;
log start filename=PA_mrbayes.log replace;
lset nst=mixed rates=gamma Ngammacat=4;
prset shapepr=exponential(0.5) clockratepr=lognormal(0.01,0.50);
set beaglesse=yes usebeagle=yes beagledevice=cpu beaglethreads=yes autoclose=yes seed=12345 swapseed=12345;
mcmc ngen=5000000 relburnin=yes burninfrac=0.25 nruns=2 nchains=4 printfreq=1000 samplefreq=1000 nchains=4 savebrlens=yes
starttree=random filename=PA.out;
sump relburnin=yes burninfrac=0.25 nruns=2 outputname=sumpoutput_v2.out;
sumt relburnin=yes burninfrac=0.25 nruns=2 ntrees=1 minpartfreq=0.05 contype=Halfcompat;
quit;
end;

Leonardo Humberto Mendoza Carbajal

unread,

Dec 29, 2017, 6:33:41 AM12/29/17

to CIPRES Science Gateway Users

Hi Mark,

Please I would like to ask also the more complex MrBayes block for CIPRES. I've tried to enter all the parameters I need into CIPRES but there are some that I cannot enter.

Thanks!!

Leonardo

Mark Miller

unread,

Dec 29, 2017, 11:43:21 AM12/29/17

to CIPRES Science Gateway Users

Hi Leonardo,

here are a couple of mrbayes blocks.
once you get the sense fo the format, you can execute anything mrbayes allows as a block.
Let me know if I cna help further.

Mark

begin mrbayes;

log start filename=concat.log;

set autoclose=yes nowarnings=no autoreplace=no;

charset Subset1 = 7337-8064\3 14718-15718\3 1-903\3;

charset Subset2 = 2-903\3 34525-35223\3 34526-35223\3;

charset Subset3 = 17788-18484\3 30606-32823\3 33645-34524\3 6555-7335\3 11014-11786\3 3-903\3;

charset Subset4 = 29959-30603\3 904-1527\3 14717-15718\3 5075-5843\3;

charset Subset5 = 905-1527\3;

charset Subset6 = 14005-14716\3 19840-20518\3 29334-29958\3 29961-30603\3 906-1527\3 23549-26441\3;

charset Subset7 = 18485-19837\3 1528-2998\3;

charset Subset8 = 1529-2998\3;

charset Subset9 = 1530-2998\3;

charset Subset10 = 2999-4258\3 7336-8064\3 22142-22838\3;

charset Subset11 = 3000-4258\3 22143-22838\3;

charset Subset12 = 22144-22838\3 16597-17785\3 3001-4258\3 7338-8064\3;

charset Subset13 = 5844-6552\3 13142-14002\3 4259-5074\3;

charset Subset14 = 6554-7335\3 9372-10258\3 4260-5074\3;

charset Subset15 = 32824-33642\3 4261-5074\3;

charset Subset16 = 5076-5843\3;

charset Subset17 = 5077-5843\3 5846-6552\3;

charset Subset18 = 11013-11786\3 5845-6552\3;

charset Subset19 = 14003-14716\3 6553-7335\3;

charset Subset20 = 8065-8785\3 21503-22141\3 8786-9370\3;

charset Subset21 = 8066-8785\3;

charset Subset22 = 8067-8785\3;

charset Subset23 = 23548-26441\3 26443-27168\3 8787-9370\3 16596-17785\3;

charset Subset24 = 8788-9370\3;

charset Subset25 = 9371-10258\3;

charset Subset26 = 9373-10258\3 20521-21502\3;

charset Subset27 = 10259-11011\3 19839-20518\3;

charset Subset28 = 21504-22141\3 10260-11011\3 11788-12370\3;

charset Subset29 = 10261-11011\3 22841-23546\3;

charset Subset30 = 11012-11786\3 28165-29331\3;

charset Subset31 = 12371-13141\3 11787-12370\3 13143-14002\3;

charset Subset32 = 11789-12370\3;

charset Subset33 = 28166-29331\3 14004-14716\3 12372-13141\3 33644-34524\3;

charset Subset34 = 27171-28164\3 28167-29331\3 12373-13141\3 13144-14002\3;

charset Subset35 = 14719-15718\3;

charset Subset36 = 15719-16594\3;

charset Subset37 = 15720-16594\3 32825-33642\3;

charset Subset38 = 15721-16594\3;

charset Subset39 = 16595-17785\3 26442-27168\3 23547-26441\3;

charset Subset40 = 19838-20518\3 29332-29958\3 17786-18484\3;

charset Subset41 = 17787-18484\3 29960-30603\3;

charset Subset42 = 18486-19837\3;

charset Subset43 = 18487-19837\3;

charset Subset44 = 20519-21502\3;

charset Subset45 = 20520-21502\3;

charset Subset46 = 21505-22141\3;

charset Subset47 = 22839-23546\3 22840-23546\3;

charset Subset48 = 26444-27168\3;

charset Subset49 = 27169-28164\3;

charset Subset50 = 27170-28164\3;

charset Subset51 = 29333-29958\3;

charset Subset52 = 30604-32823\3 33643-34524\3;

charset Subset53 = 30605-32823\3;

charset Subset54 = 32826-33642\3;

charset Subset55 = 34527-35223\3;

partition PartitionFinder = 55:Subset1, Subset2, Subset3, Subset4, Subset5, Subset6, Subset7, Subset8, Subset9, Subset10, Subset11, Subset12, Subset13, Subset14, Subset15, Subset16, Subset17, Subset18, Subset19, Subset20, Subset21, Subset22, Subset23, Subset24, Subset25, Subset26, Subset27, Subset28, Subset29, Subset30, Subset31, Subset32, Subset33, Subset34, Subset35, Subset36, Subset37, Subset38, Subset39, Subset40, Subset41, Subset42, Subset43, Subset44, Subset45, Subset46, Subset47, Subset48, Subset49, Subset50, Subset51, Subset52, Subset53, Subset54, Subset55;

set partition=PartitionFinder;

lset applyto=(1) nst=6 rates=invgamma;

lset applyto=(2) nst=6 rates=invgamma;

lset applyto=(3) nst=6 rates=gamma;

lset applyto=(4) nst=6 rates=invgamma;

lset applyto=(5) nst=6 rates=gamma;

lset applyto=(6) nst=6 rates=gamma;

lset applyto=(7) nst=6 rates=gamma;

lset applyto=(8) nst=6 rates=gamma;

lset applyto=(9) nst=6 rates=gamma;

lset applyto=(10) nst=6 rates=gamma;

lset applyto=(11) nst=6 rates=gamma;

lset applyto=(12) nst=6 rates=gamma;

lset applyto=(13) nst=6 rates=invgamma;

lset applyto=(14) nst=6 rates=gamma;

lset applyto=(15) nst=6 rates=invgamma;

lset applyto=(16) nst=6 rates=invgamma;

lset applyto=(17) nst=6 rates=gamma;

lset applyto=(18) nst=6 rates=invgamma;

lset applyto=(19) nst=6 rates=invgamma;

lset applyto=(20) nst=6 rates=invgamma;

lset applyto=(21) nst=6 rates=invgamma;

lset applyto=(22) nst=6 rates=gamma;

lset applyto=(23) nst=6 rates=invgamma;

lset applyto=(24) nst=6 rates=gamma;

lset applyto=(25) nst=6 rates=gamma;

lset applyto=(26) nst=6 rates=gamma;

lset applyto=(27) nst=6 rates=invgamma;

lset applyto=(28) nst=6 rates=invgamma;

lset applyto=(29) nst=6 rates=gamma;

lset applyto=(30) nst=6 rates=invgamma;

lset applyto=(31) nst=6 rates=invgamma;

lset applyto=(32) nst=6 rates=gamma;

lset applyto=(33) nst=6 rates=invgamma;

lset applyto=(34) nst=6 rates=gamma;

lset applyto=(35) nst=6 rates=invgamma;

lset applyto=(36) nst=6 rates=invgamma;

lset applyto=(37) nst=6 rates=gamma;

lset applyto=(38) nst=6 rates=gamma;

lset applyto=(39) nst=6 rates=invgamma;

lset applyto=(40) nst=6 rates=gamma;

lset applyto=(41) nst=6 rates=gamma;

lset applyto=(42) nst=6 rates=invgamma;

lset applyto=(43) nst=6 rates=gamma;

lset applyto=(44) nst=6 rates=gamma;

lset applyto=(45) nst=6 rates=gamma;

lset applyto=(46) nst=6 rates=gamma;

lset applyto=(47) nst=6 rates=invgamma;

lset applyto=(48) nst=6 rates=gamma;

lset applyto=(49) nst=6 rates=invgamma;

lset applyto=(50) nst=6 rates=invgamma;

lset applyto=(51) nst=6 rates=invgamma;

lset applyto=(52) nst=6 rates=invgamma;

lset applyto=(53) nst=6 rates=invgamma;

lset applyto=(54) nst=6 rates=gamma;

lset applyto=(55) nst=6 rates=gamma;

prset applyto=(all) ratepr=variable;

unlink statefreq=(all) revmat=(all) shape=(all) pinvar=(all) tratio=(all);

showmodel;

mcmcp

ngen=50000000

filename=concat_iguania

nruns=2

nchains=4

temp=0.2

samplefreq=5000

printfreq=5000

Mcmcdiagn=yes

Diagnfreq=1000

savebrlens=yes

checkpoint=yes

checkfreq=200

append=no;

mcmc;

sumt burnin=0.20 cont=all;

sump burnin=0.20;

end;

begin mrbayes;

log start filename="sinRag1sreloj.log" append;

charset cytb= 1-1034;

charset 16s= 1035-1462;

charset 12s= 1463-1869;

charset COI= 1870-2522;

charset ND4= 2523-3175;

charset Rag2=3176-3810;

charset Cmos=3811-4350;

charset R35= 4351-5389;

partition favored=8: cytb,16s,12s,COI,ND4,Rag2,Cmos,R35;

[settings evol model]

set partition=favored;

lset applyto=(1) nucmodel=4by4 nst=6 rates=gamma;

prset applyto=(1) statefreqpr=fixed(0.3615,0.3598,0.0559,0.2228) shapepr=fixed(0.471) revmatpr=fixed(1,15.895,1,1,12.6037, 1) ;

lset applyto=(2) nucmodel=4by4 nst=6 rates=invgamma ;

prset applyto=(2) statefreqpr=fixed(0.3548,0.2549,0.1441,0.2462) revmatpr=fixed(7.0129,24.1607,7.0129,1,52.3083, 1) shapepr=fixed(0.68) pinvarpr=fixed(0.312);

lset applyto=(3) nucmodel=4by4 nst=6 rates=invgamma ;

prset applyto=(3) statefreqpr=fixed(0.385,0.2154,0.1706,0.229) revmatpr=fixed(8.5822,27.1476,8.5822,1,107.8665, 1) shapepr=fixed(0.707) pinvarpr=fixed(0.275);

lset applyto=(4) nucmodel=4by4 nst=6 rates=invgamma ;

prset applyto=(4) statefreqpr=fixed(0.353,0.2956,0.0711,0.2803) revmatpr=fixed(0.473,14.1203,0.473,1,8.2516, 1) shapepr=fixed(0.655) pinvarpr=fixed(0.461);

lset applyto=(5) nucmodel=4by4 nst=6 rates=invgamma ;

prset applyto=(5) statefreqpr=fixed(0.4075,0.3153,0.0405,0.2367) revmatpr=fixed(0.2298,10.0533,0.2298,1,4.8493, 1) shapepr=fixed(0.628) pinvarpr=fixed(0.183) ;

lset applyto=(6) nucmodel=4by4 nst=2 rates=gamma ;

prset applyto=(6) statefreqpr=fixed(0.3135,0.1913,0.2264,0.2688) revmatpr=fixed(1,1,1,1,1, 1) shapepr=fixed(0.503) Tratiopr=fixed(2.6206);

lset applyto=(7) nucmodel=4by4 nst=2 rates=gamma ;

prset applyto=(7) statefreqpr=fixed(equal) shapepr=fixed(0.639) Tratiopr=fixed(3.1353);

lset applyto=(8) nucmodel=4by4 nst=6 rates=invgamma ;

prset applyto=(8) statefreqpr=fixed(0.2893,0.1771,0.2083,0.3253) revmatpr=fixed(1,3.4602,0.7911,0.7911,3.4602, 1) shapepr=fixed(1.703);

unlink statefreq=(all) revmat=(all) shape=(all) pinvar=(all);

prset applyto=(all) ratepr=variable;

[Groups]

outgroup Podocnemis_unifilis;

constraint root=1-.;

constraint Chelydae=Chelus_finbriatus Erymnochelys_madagascariensis Podocnemis_unifilis Pelusios_castaneous;

constraint Trionychya=Apalone_spinifera Apalone_ferox Amyda_ornata Amyda_cartilaginea;

constraint Apalone=Apalone_spinifera Apalone_ferox;

constraint Amyda=Amyda_ornata Amyda_cartilaginea;

constraint Kinosternidae=Kinosternon_flavescens Kinosternon_subrubrum Sternotherus_carinatus Staurotypus_triporcatus;

constraint Trachemys=Trachemys_adiutrix Trachemys_callirostris Trachemys_decorata Trachemys_decussata Trachemys_dorbigni Trachemys_emolli Trachemys_gaigeae Trachemys_nebulosa Trachemys_ornata Trachemys_scripta Trachemys_stejnegeri Trachemys_taylori Trachemys_terrapen Trachemys_venusta Trachemys_yaquia;

constraint Terrapene=Terrapene_carolina Terrapene_coahuila Terrapene_mexicana Terrapene_nelsoni Terrapene_ornata;

constraint Pseudemys=Pseudemys_alabamensis Pseudemys_concinna Pseudemys_floridana Pseudemys_gorzugi Pseudemys_nelsoni Pseudemys_peninsularis Pseudemys_rubriventris Pseudemys_suwanniensis Pseudemys_texana;

constraint Graptemys=Graptemys_barbouri Graptemys_caglei Graptemys_ernsti Graptemys_flavimaculata Graptemys_geographica Graptemys_gibbonsi Graptemys_nigrinoda Graptemys_oculifera Graptemys_ouachitensis Graptemys_pseudogeographica Graptemys_pulchra Graptemys_versa;

constraint Glyptemys=Glyptemys_insculpta Glyptemys_muhlenbergii;

constraint Emys=Emys_orbicularis Emys_trinacris;

constraint Chrysemys=Chrysemys_dorsalis Chrysemys_picta;

constraint Emydidae=Actinemys_marmorata Chrysemys_dorsalis Chrysemys_picta Clemmys_guttata Deirochelys_reticularia Emydoidea_blandingii Emys_orbicularis Emys_trinacris Glyptemys_insculpta Glyptemys_muhlenbergii Graptemys_barbouri Graptemys_caglei Graptemys_ernsti Graptemys_flavimaculata Graptemys_geographica Graptemys_gibbonsi Graptemys_nigrinoda Graptemys_oculifera Graptemys_ouachitensis Graptemys_pseudogeographica Graptemys_pulchra Graptemys_versa Malaclemys_terrapin Pseudemys_alabamensis Pseudemys_concinna Pseudemys_floridana Pseudemys_gorzugi Pseudemys_nelsoni Pseudemys_peninsularis Pseudemys_rubriventris Pseudemys_suwanniensis Pseudemys_texana Terrapene_carolina Terrapene_coahuila Terrapene_mexicana Terrapene_nelsoni Terrapene_ornata Trachemys_adiutrix Trachemys_callirostris Trachemys_decorata Trachemys_decussata Trachemys_dorbigni Trachemys_emolli Trachemys_gaigeae Trachemys_nebulosa Trachemys_ornata Trachemys_scripta Trachemys_stejnegeri Trachemys_taylori Trachemys_terrapen Trachemys_venusta Trachemys_yaquia;

constraint Kinixys=Kinixys_belliana Kinixys_erosa Kinixys_homeana Kinixys_lobatsiana Kinixys_natalensis Kinixys_nogueyi Kinixys_spekii Kinixys_zombensis;

constraint Gopherus=Gopherus_polyphemus Gopherus_agassizii Gopherus_berlandieri Gopherus_evgoodei Gopherus_flavomarginatus Gopherus_morafkai;

constraint Testudinidae=Aldabrachelys_gigantea Astrochelys_radiata Astrochelys_yniphora Centrochelys_sulcata Chelonoidis_abingdonii Chelonoidis_alburyorum Chelonoidis_becki Chelonoidis_carbonarius Chelonoidis_chathamensis Chelonoidis_chilensis Chelonoidis_darwini Chelonoidis_denticulatus Chelonoidis_duncanensis Chelonoidis_hoodensis Chelonoidis_nigra Chelonoidis_phantastica Chelonoidis_porteri Chelonoidis_vicina Chersina_angulata Dipsochelys_arnoldi Dipsochelys_hololissa Geochelone_elegans Geochelone_platynota Gopherus_agassizii Gopherus_berlandieri Gopherus_evgoodei Gopherus_flavomarginatus Gopherus_morafkai Gopherus_polyphemus Homopus_areolatus Homopus_boulengeri Homopus_femoralis Homopus_signatus Homopus_solus Indotestudo_elongata Indotestudo_forstenii Indotestudo_travancorica Kinixys_belliana Kinixys_erosa Kinixys_homeana Kinixys_lobatsiana Kinixys_natalensis Kinixys_nogueyi Kinixys_spekii Kinixys_zombensis Malacochersus_tornieri Manouria_emys Manouria_impressa Psammobates_geometricus Psammobates_oculiferus Psammobates_tentorius Pyxis_arachnoides Pyxis_planicauda Stigmochelys_pardalis Testudo_graeca Testudo_hermanni Testudo_horsfieldii Testudo_kleinmanni Testudo_marginata Testudo_werneri;

constraint EuroAsiatico=Batagur_affinis Batagur_baska Batagur_borneoensis Batagur_cambodia Batagur_dhongoka Batagur_kachuga Batagur_trivittata Cuora_amboinensis Cuora_aurocapitata Cuora_bourreti Cuora_flavomarginata Cuora_galbinifrons Cuora_mccordi Cuora_mouhotii Cuora_pani Cuora_picturata Cuora_serrata Cuora_trifasciata Cuora_yunnanensis Cuora_zhoui Cyclemys_atripons Cyclemys_dentata Cyclemys_fusca Cyclemys_gemeli Cyclemys_oldhamii Cyclemys_pulchristriata Cyclemys_tcheponensis Geoclemys_hamiltonii Geoemyda_japonica Geoemyda_spengleri Hardella_thurjii Heosemys_annandalii Heosemys_depressa Heosemys_grandis Heosemys_spinosa Leucocephalon_yuwonoi Malayemys_khoratensis Malayemys_macrocephala Malayemys_subtrijuga Mauremys_annamensis Mauremys_caspica Mauremys_guangxiensis Mauremys_iversoni Mauremys_japonica Mauremys_leprosa Mauremys_megalocephala Mauremys_mutica Mauremys_nigricans Mauremys_pritchardi Mauremys_reevesii Mauremys_rivulata Mauremys_sinensis Melanochelys_tricarinata Melanochelys_trijuga Morenia_ocellata Morenia_petersi Notochelys_platynota Ocadia_philippeni Orlitia_borneensis Pangshura_smithii Pangshura_sylhetensis Pangshura_tecta Sacalia_bealei Sacalia_pseudocellata Sacalia_quadriocellata Siebenrockiella_crassicollis Siebenrockiella_leytensis Vijayachelys_silvatica;

constraint Batagur=Batagur_affinis Batagur_baska Batagur_borneoensis Batagur_cambodia Batagur_dhongoka Batagur_kachuga Batagur_trivittata;

constraint Cuora=Cuora_amboinensis Cuora_aurocapitata Cuora_bourreti Cuora_flavomarginata Cuora_galbinifrons Cuora_mccordi Cuora_mouhotii Cuora_pani Cuora_picturata Cuora_serrata Cuora_trifasciata Cuora_yunnanensis Cuora_zhoui;

constraint Geoemyda=Geoemyda_japonica Geoemyda_spengleri;

constraint Mauremys=Mauremys_annamensis Mauremys_caspica Mauremys_guangxiensis Mauremys_iversoni Mauremys_japonica Mauremys_leprosa Mauremys_megalocephala Mauremys_mutica Mauremys_nigricans Mauremys_pritchardi Mauremys_reevesii Mauremys_rivulata Mauremys_sinensis;

constraint Rhinoclemmys=Rhinoclemmys_annulata Rhinoclemmys_areolata Rhinoclemmys_diademata Rhinoclemmys_funerea Rhinoclemmys_melanosterna Rhinoclemmys_nasuta Rhinoclemmys_pulcherrima Rhinoclemmys_punctularia Rhinoclemmys_rubida;

constraint Geoemydidae=Batagur_affinis Batagur_baska Batagur_borneoensis Batagur_cambodia Batagur_dhongoka Batagur_kachuga Batagur_trivittata Cuora_amboinensis Cuora_aurocapitata Cuora_bourreti Cuora_flavomarginata Cuora_galbinifrons Cuora_mccordi Cuora_mouhotii Cuora_pani Cuora_picturata Cuora_serrata Cuora_trifasciata Cuora_yunnanensis Cuora_zhoui Cyclemys_atripons Cyclemys_dentata Cyclemys_fusca Cyclemys_gemeli Cyclemys_oldhamii Cyclemys_pulchristriata Cyclemys_tcheponensis Geoclemys_hamiltonii Geoemyda_japonica Geoemyda_spengleri Hardella_thurjii Heosemys_annandalii Heosemys_depressa Heosemys_grandis Heosemys_spinosa Leucocephalon_yuwonoi Malayemys_khoratensis Malayemys_macrocephala Malayemys_subtrijuga Mauremys_annamensis Mauremys_caspica Mauremys_guangxiensis Mauremys_iversoni Mauremys_japonica Mauremys_leprosa Mauremys_megalocephala Mauremys_mutica Mauremys_nigricans Mauremys_pritchardi Mauremys_reevesii Mauremys_rivulata Mauremys_sinensis Melanochelys_tricarinata Melanochelys_trijuga Morenia_ocellata Morenia_petersi Notochelys_platynota Ocadia_philippeni Orlitia_borneensis Pangshura_smithii Pangshura_sylhetensis Pangshura_tecta Rhinoclemmys_annulata Rhinoclemmys_areolata Rhinoclemmys_diademata Rhinoclemmys_funerea Rhinoclemmys_melanosterna Rhinoclemmys_nasuta Rhinoclemmys_pulcherrima Rhinoclemmys_punctularia Rhinoclemmys_rubida Sacalia_bealei Sacalia_pseudocellata Sacalia_quadriocellata Siebenrockiella_crassicollis Siebenrockiella_leytensis Vijayachelys_silvatica;

[ points]

calibrate

root=lognormal(155.7,180)

Chelydae= offsetlognormal(70.6,77.5,80)

Chelus_finbriatus=offsetgamma(5.3,8.4,80)

Trionychya=offsetlognormal(130,133.2,80)

Apalone=offsetlognormal(46.2,48.25,80)

Apalone_spinifera=offsetgamma(4.9,7.45,80)

Apalone_ferox=offsetgamma(1.8,3.35,80)

Amyda=offsetlognormal(16,18.2,80)

Kinosternidae=offsetlognormal(70.6,77.5,80)

Kinosternon_flavescens=offsetgamma(4.9,7.6,80)

Kinosternon_subrubrum=offsetgamma(1.8,3.35,80)

Chelydra_serpentina=offsetgamma(1.8,3.35,80)

Caretta_caretta=offsetgamma(0.3,1.05,80)

Trachemys=offsetlognormal(70.6,77.5,80)

Trachemys_scripta=offsetgamma(4.9,7.6,80)

Terrapene=offsetlognormal(13.6,14.8,80)

Pseudemys=offsetlognormal(10.3,11.95,80)

Graptemys=offsetlognormal(33.3,633.,80)

Graptemys_geographica=offsetgamma(0.3,1.05,80)

Glyptemys=offsetlognormal(13.6,14.8,80)

Glyptemys_insculpta=offsetgamma(0.012,1.3,80)

Glyptemys_muhlenbergii=offsetgamma(0.3,1.05,80)

Emys=offsetlognormal(16,18.2,80)

Actinemys_marmorata=offsetgamma(4.9,7.6,80)

Chrysemys=offsetlognormal(13.6,14.8,80)

Malaclemys_terrapin=offsetgamma(0.0,0.05,80)

Emydoidea_blandingii=offsetgamma(4.9,7.6,80)

Kinixys=offsetlognormal(2.3,3.95,80)

Gopherus=offsetlognormal(33.2,35.5,80)

Gopherus_polyphemus=offsetgamma(0.3,1.05,80)

Homopus_signatus=offsetgamma(0.012,1.3,80)

Testudo_hermanni=offsetlognormal(0.012,1.3,80)

Stigmochelys_pardalis=offsetgamma(2.3,3.95,80)

Testudinidae=offsetlognormal(58.7,60.2,80)

EuroAsiatico=offsetlognormal(48.6,55.2,80)

Batagur=offsetlognormal(0.8,1.7,80)

Cuora=offsetlognormal(5.3,7,80)

Geoemyda=offsetlognormal(23,25.7,80)

Mauremys=offsetlognormal(33.9,35.5,80)

Rhinoclemmys=offsetlognormal(16,18.2,80)

Geoemydidae=offsetlognormal(50.3,53.03,80)

Mauremys_mutica=offsetgamma(3.6,4.45,80)

Mauremys_caspica=offsetgamma(5.3,8.45,80);

[settings priors reloj estricto arboles con la misma probabilidadd]

prset nodeagepr=calibrated;

prset brlenspr=clock:birthdeath;

prset fossilizationpr=beta(1,1);

prset speciationpr=exp(0.25);

prset extinctionpr=beta(1,1);

prset sampleprob=0.0005;

prset samplestrat=diversity;

prset clockvarpr=strict;

prset topologypr=uniform;

[settings run]

mcmcp Ngen=200000000 Nruns=2 Nchains=4 Temp=0.2 Samplefreq=5000 Printfreq=5000 Printall=yes savebrlens=yes relburnin=yes burninfrac=0.30;

mcmc;

sumt;

sump;

END;

Leonardo Humberto Mendoza Carbajal

unread,

Jan 5, 2018, 2:59:40 AM1/5/18

to CIPRES Science Gateway Users

Hi Mark,

Thanks a lot!!

Happy new year!

Leonardo

Mark Miller

unread,

Jan 5, 2018, 9:24:03 AM1/5/18

to CIPRES Science Gateway Users

Happy New Year to you as well!

Mark

kasal...@gmail.com

unread,

Jul 8, 2020, 10:12:15 AM7/8/20

to CIPRES Science Gateway Users

Dear,

tanks for all exemples.

I am using a constraint taxa with numbers: (7:1,(((36:1,54:1):1,(142.......

my dubs is where and which headline I use for specified the taxa names inside my file to run MB in Cipres ? I put as name Polyphaga_contree from my file constraint done in Mesquite but for running MB in CIPRES I put all comandes in one file, so I dont know if name is necessary here.

Outgroup NC_0365

mcmc ngen = 10000000 printfreq = 1000 samplefreq = 200 nchains = 4 savebrlens = yes;

mcmc;

constraint polyph_contree = (7:1,(((36:1,54:1):1,(142:1,143:1):1):1,(((19:1,26:1):1,28:1):1,((((148:1,156:1):1,168:1):1,(161:1,165:1):1):1,(175:1,176:1):1):1):1):1):1;

prset topologypr = constraints(polyph_contree)

sump burnin=12500;

sumt burnin=12500;

quit;

END;

kasal...@gmail.com

unread,

Jul 8, 2020, 10:12:53 AM7/8/20

to CIPRES Science Gateway Users

thanks in advance for the advices

Mark Miller

unread,

Jul 8, 2020, 4:30:56 PM7/8/20

to CIPRES Science Gateway Users

Hi there,

Thanks for the question. This can be answered using the MB manual.

I would start here:

The constraints option allows you to specify complicated prior probabilities on trees (constraints are discussed more fully in "help constraint"). Note that you must specify a list of constraints that you wish to be obeyed. The list can be either the constraints' name or number. Finally, you can fix the topology to that of a user tree defined in a trees block. Branch lengths will still be sampled as usual on the fixed topology.

This section describes creating a trees block.
Commands that should be in a NEXUS file (data block, trees block or taxa block) include: Begin -- Denotes beginning of block in file Dimensions -- Defines size of character matrix End -- Denotes end of a block in file Endblock -- Alternative way of denoting end of a block Format -- Defines character format in data block Matrix -- Defines matrix of characters in data block Taxlabels -- Defines taxon labels Translate -- Defines alternative names for taxa Tree -- Defines a tree Note that this program supports the use of the shortest unambiguous spelling of the above commands (e.g., "exe" instead of "execute"). ---------------------------------------------------------------------------

Reply all

Reply to author

Forward