#NEXUS [written Sun May 04 15:54:34 PDT 2008 by Mesquite version 2.01+ (build j65) at Thrandina.local/10.0.1.8 (Wayne Maddison)] BEGIN TAXA; TITLE Untitled_Block_of_Taxa; DIMENSIONS NTAX=16; TAXLABELS taxon_0 taxon_1 taxon_2 taxon_3 taxon_4 taxon_5 taxon_6 taxon_7 taxon_8 taxon_9 taxon_10 taxon_11 taxon_12 taxon_13 taxon_14 taxon_15 ; BLOCKID WM114cbdd482a17; END; BEGIN CHARACTERS; TITLE 'Matrix in file "09-pcaSim.nex"'; DIMENSIONS NCHAR=50; FORMAT DATATYPE = CONTINUOUS; MATRIX taxon_0 2.992210463104165 -0.5213796212123114 -3.1933608712155848 -0.2380414477440551 3.069338067864813 0.6350921841170124 -2.6503509149104265 2.641646658530784 -5.059102625151112 -2.4386173699395433 2.5845701126632075 -2.0473976448968 -3.596960412307545 -0.8637710076749665 5.1307348768653815 -2.2774077261335 -5.772428413201568 -1.6210860251077548 -7.018314185792198 1.2784880654198518 0.26418598552638706 -2.962340357371817 -0.7451474147272754 -0.12016682211005533 1.333832991953333 -1.9820220917458642 1.7819622217844668 -0.4286168252544469 1.795046083754058 2.652213421504545 7.670205132731681 -0.7248674817380841 -2.0387807702867287 0.04071691899388907 3.1885224136085624 1.5326956826410756 -2.0411192380664396 1.0679997564600734 -2.9737368765346073 -0.998993949808622 3.8772535941999644 -2.899050659307263 3.111940122414367 -0.5078757021126066 -2.5555512348818663 -1.2496058031291895 -5.3209135461338 -3.2132506109745234 0.1760345130555176 -1.2041429276738413 taxon_1 -0.6159089185463594 2.8251237433505123 5.966914902224667 -1.3176328349660005 2.0941476552549565 0.44826630641625714 1.3996089919193146 -1.8532609049922442 1.194787888600039 3.1995846401899177 -3.3767991782135516 4.078721540595769 -1.8825066729903543 -2.1790587847454193 -2.341422971612696 -1.7221567195257916 6.488290666168001 -2.8157613471956098 2.140899424517751 7.42031539664155 3.1089578391529162 5.192756964318315 5.125858723642327 2.7855834150038055 -4.088988914259199 0.7636339756999861 6.710092803875183 6.080042718269267 -2.2331917282182645 4.378059635370082 -5.854460369408296 2.2949346974108815 1.6304418921819874 -2.9655391285075803 -3.550215162582551 4.141724864215471 1.6724873281164618 -5.767240631997499 2.170324163357657 -5.947640512522238 -0.853892797640129 -1.6393046633934993 -1.681871628707285 -4.301288081573986 8.734936776882801 3.1552145420177706 0.7470128600815709 5.353776200346818 -3.69307480676989 7.680837068321763 taxon_2 6.3624224064335975 1.8173101565294902 2.171088928715866 6.823934646313486 2.2604710950087457 3.8337119064827956 -6.464618023811242 3.1187400284883946 -1.046349744590067 -3.2087683040313095 -6.052522276296489 -0.7366381903523069 -6.31561123183821 -3.2944871838806615 0.9988153898179807 2.4419823617890932 -2.6115945171794124 -4.608438307935261 -1.363071804984885 -0.6911421370388441 6.866530892676542 2.8513577200354208 -2.433151696664187 -5.489272271532662 -2.308495464191093 -0.3591372230630081 2.1454965658865173 -0.1405526436443364 -0.9079738877819615 -4.6259610962668125 0.9964725009164546 -4.240685963370481 -2.316711789201114 4.777333012172514 -2.870476246718841 -3.496157826015133 -0.7184304266330752 6.872332691482216 -1.9468183051415946 3.98885173925657 -1.0494559525880875 2.8724559133094933 4.969518251272572 0.4783460019249923 6.429282273299414 6.667713665123945 -4.310152955576827 -1.8853842165643402 -2.523165702455672 -5.408622702797826 taxon_3 -5.201832848109966 -0.8746546751985125 4.859598341823185 -10.96477642311772 1.5204975201441648 1.3578425910414385 -2.2199189338672234 1.590256816332689 7.017491272025122 4.245976423341276 -3.278078452270021 1.6127812289970946 -4.607341873331669 -6.342903750993334 1.1298613943032256 -2.2320638717399603 2.315516487815637 -1.1952732127851067 4.335321394945093 4.36985762581831 0.8958525707555314 -3.9862985905926784 1.693317382658954 9.374992707026973 -2.4880839144774765 4.536915777338344 7.469573529327107 8.643267530626225 -3.16000655473264 1.3954298404783216 -4.113924716943122 1.1366911018712405 2.7523379648453075 0.21135894125504628 4.66810055665416 0.7893507224353902 4.589855965337723 -4.278243171177458 3.63432601371945 -2.350802018907585 -1.4587449773852095 -6.259644681624157 2.5444343937677902 -7.697645113969953 3.742946579512064 0.04135799879604185 3.570952158983406 1.7621666786331083 -2.9974881881740187 1.5799927778122225 taxon_4 -6.463485243641799 4.94421175499709 -2.853757463987187 3.3594087843644296 -1.5720253151370036 -4.99154712449598 7.825025262470588 -2.69097154924848 0.9841281873137764 -3.8362660792611787 -0.8817197347999509 -3.71810933723565 -8.94599184468518 1.1710322609471149 4.839513930438739 -5.970074190286658 0.3808855996973477 -0.07046063869206298 -0.5306946781829824 4.267848017580845 0.08983407407248434 -0.5579010333999708 -3.3421800569495304 8.319564395358586 1.7980669328726966 3.6972341143861303 7.4051818138182695 -1.5260887750935135 1.8488665987483048 -5.332055526132642 5.446796765387883 -1.1016534505101219 -5.685088511958088 -0.37730923776840575 -1.5411057363920837 6.961987939616119 -0.7714668846801699 5.490664733312178 -3.039117581377806 -1.4648632340854641 3.646512282679773 -9.78469566471315 -5.5644934027800375 -1.230497641353347 -4.9898982452553575 5.242606137274956 -0.3204028433951678 -2.1249965693539936 2.5926826825318043 -9.134354498947674 taxon_5 -3.235189667445917 -3.2074435127789394 -1.515072637351711 5.129019140711172 -0.2511919982420254 -6.004518295536943 9.66948839642005 -4.305809631395871 -4.847624054233453 -0.019721192643707197 -3.983032444626711 -4.866030864332769 -9.028562085137592 1.692067880252972 -1.9474799446120752 -7.434833286186466 -0.3539631783105346 -1.9777517687377841 0.9263836526145435 7.830049530228649 11.109393642392627 -3.74592278002007 -2.163920230281321 2.9687399740306013 -6.777474784216082 -5.322313846555923 7.258038267455178 -5.177603878943359 -1.908998404527779 0.25813938887819 0.6333061210851874 1.0711186553740437 -6.903208109120726 0.9941867144290049 -0.14000148092968423 2.3208278691450874 -4.914557108457754 3.5447366795977864 4.1283509266230265 -3.2831214257398176 5.9103613150160985 -3.2025366156073205 -0.4001808473123094 2.596724457843293 -7.702654707396869 3.278044663533515 0.458953542970562 1.6010084701173213 10.905687347874137 -7.410017297084473 taxon_6 -3.699479960972744 4.53800427959125 -2.066932104434697 8.985412472537655 0.22039166638329655 1.824272563477916 4.008793941929678 2.8248272016958165 -3.633177666559673 -6.540269125459169 -3.9091653752985 -3.1397185490353112 -5.004209616382209 6.245979201979994 -1.927228911994047 -2.2490196459708045 0.7092262026234639 2.8428511039597852 -5.027495383570602 0.54423943799513 -1.5850516247688553 -5.813920464408541 -1.9723175646893893 3.297508287197868 -4.121890237272859 -2.1906672137515715 -2.5647212409844724 -1.6040360378366836 2.13177753393053 -6.408858105884415 1.2891309412441374 1.159769290515452 0.04119556823555648 -4.306619046793046 0.22237859027133045 7.011731365372389 3.1367530556712753 -1.9851973867177128 -2.4508170817723887 -4.179998157792248 8.290017641640908 0.6434311372363434 -4.687921596081729 2.8046111244041048 -0.8212456294152074 0.8542866895157324 -2.550371316789558 -3.475989938975587 -3.816752514051866 -2.5563811563332566 taxon_7 -5.148929648774498 3.469933541841339 -2.3186344332896605 3.6093098490172038 0.44895247644908265 -9.684672098815653 10.145395609629364 -3.26196348111565 5.347583658716699 0.9412173429168371 -0.8176574653090629 -10.502749274710565 -14.584748449032737 -2.6917146090965565 5.6161136222092605 -10.434823776983642 -1.7715389666415304 -1.4385622858509435 1.5226896377309767 5.927830656878157 7.239808551702298 -0.15869558258888583 0.8629857843416985 4.64370493773493 1.5648211067744155 8.93824681742173 8.895404469816059 -2.177123905866375 -1.7103721197666366 -6.602830326503024 1.2309272851169513 3.7146983877013895 -4.855818138295894 -0.2252627917708439 -8.115511824914407 4.338287136319063 -6.720081127523443 6.416844525001331 4.49308944854158 -7.083634541394531 2.5089316886864745 -6.702409638452657 0.19601033616538976 1.5557246759426095 -5.218385387184489 1.2082685579206967 0.49503937117442876 0.38287176930953737 1.018833363453828 -5.321456696487146 taxon_8 0.5722443579091707 -0.10995907911662861 4.142286055744222 -3.0658070631071928 -0.4237265275489378 -1.8586288766488512 -4.053685422166835 -3.840380447936093 4.0638687078249 6.49228400466243 -2.091839846655442 4.646385456665855 -1.9443277487898516 -2.5977470505629467 5.044187992455365 -2.4210148238386133 2.292875746434741 0.546034857502701 -0.3262725062405689 6.269070297191394 -1.2105885924562547 4.20147718304619 2.8483200600485388 6.640649744753104 -1.0166497375739931 -0.6168057373425577 2.802816891407057 5.6335378581461715 -4.436877016882855 4.774458486072696 -1.4496484694521472 1.8227134443750517 4.281167312683058 -0.9693655585960292 1.7767277989832924 -1.0043744338204683 3.4581151609932195 -3.907664272216942 6.277856072904209 -5.678128970133203 0.970806719582655 -1.148595450893969 -0.9629984532534221 -0.42575843588267354 0.80466624979038 1.0870477874947486 2.098260781194403 0.9862965537506282 -6.715050890023075 -0.11350041111422549 taxon_9 -4.18262041797215 -2.7649886913304043 1.4296463397605161 -3.834727817597635 -0.465590068878241 -0.5383941766816311 -3.0284871108972857 -0.05629736619712772 5.980846426317518 6.825308412516355 -0.6900213963766032 2.7136291950043843 -2.7004152031103774 -3.4338999702432953 2.658337210121168 -3.0975278146446006 -1.7380400754317402 -1.365382508623073 3.834122630902766 7.615596786355233 -1.5221612800014603 -1.577214469703946 -0.31673152895328616 6.752084381819787 0.24461320894275657 4.037798399853933 5.808789032023899 4.2815304320779095 -2.181840473372508 4.253745342623702 -2.725347544736437 4.342768303330084 4.121397685587703 -1.8195658767499012 4.676486291813086 1.453794374527704 3.107702019551842 -5.565687411153125 3.3701235064099544 -2.2844406087780897 -0.3554008961264512 -2.4177120633980413 0.3228108805838046 -0.29163145002290114 0.5683905489267493 1.283861378806837 0.9450795587308347 0.815700672451076 -4.759441020156112 4.2019460646146 taxon_10 -0.7984014847917035 1.6645953040765509 -4.08077316600221 0.5373688677972157 1.490446117783925 -6.812190477068703 2.1380651790565577 0.07832692810750519 -1.5096393046752625 -6.498260815558502 -1.4702800155479006 0.028669847647889907 1.585379176078419 1.2633909156979837 -0.6905822798896253 0.05225244049801159 -0.9525178185661819 -2.5093527839800593 2.302359434929261 -3.373671143806518 5.1338367288843285 1.8789082289101515 -1.1449802406029406 4.520948211663615 -1.1678097468707889 -0.7658518677083612 0.4497266370331603 -5.005327975681178 0.593240537245384 -2.0624172877118467 10.525509652614799 -0.599110787120124 -1.03270007414403 -0.31088243244214075 4.77982135255517 7.048737433841094 -1.312648114112734 -3.1376720216818557 -2.3064278823111657 -0.7501611475794598 5.7938911994163655 -7.481930652870725 1.3884792914308703 0.2572156830074199 -0.5076956209592047 -3.015825908499033 4.47022547587248 -1.579576621829398 4.1163645780542275 0.061883852540211226 taxon_11 0.8360500930032865 3.7199644983362923 0.8451499732199488 7.4818579577105 -1.0788236234014275 0.9188853348675519 1.445067483480759 2.240917547533641 -3.825385769102208 -4.29889774641609 -6.324924163469797 -0.3145366572930186 -3.536017745052546 4.6853033878729455 -3.3298969876877558 -1.8119059547310918 -1.0305078754774941 2.161933705234238 -1.7718765640333531 1.2712904388409343 4.763405909619582 -5.7093921476256675 -4.981564546902445 6.121266970969877 -2.282250438289009 2.445126736867549 -1.2451583651096034 -1.1828835533344537 1.2486308790946352 -6.623605334113291 2.2704339787976133 -3.6170579181190803 -2.030218595278567 -5.1730977540793495 -0.7401932053653907 6.716142711271315 1.9303172645517237 0.22175035345217733 -6.975720326731873 -4.223297009344084 8.08626228074618 -0.9205858140102456 -2.4018308165632516 0.8272501165982016 -1.8689344091900828 0.952587616047728 -2.841501788436332 -2.2955602425886656 -3.3547123546310322 -1.4262039345594535 taxon_12 4.093418494872468 5.122811167228835 2.962067090000816 -0.3600342333113205 0.9845813939315629 1.3035777162553865 -1.607453932576031 0.3042689605306027 0.702455139273628 -3.3876169410138735 2.8641999351798066 3.174504680969588 -2.4488867416498348 2.2208158459534624 3.394037784646745 1.1269568659015419 5.588532817310609 -1.4239330049474042 0.4086880297748585 5.516669947018912 -0.42917631464815875 -0.2298713899902407 -0.30193982470331693 4.449894363161521 1.3684477293560398 -0.2584869576795583 5.163055127771319 6.682193195089983 1.821489898417851 -1.2115230296563029 1.9304448283708402 2.5533596147724285 3.8661408417466 -1.0861053830104712 -0.8060576625208266 0.7786870005069308 -0.06703151381538142 -2.768442083431684 4.306129260224428 -3.348528878626742 2.2054130229740574 -6.006312148040669 1.914522339691292 1.1273343750937705 -3.1664435644141706 1.4390866252447188 1.9178930612671765 5.140262578774443 -7.944489482726189 4.979348519651387 taxon_13 -8.617383286913775 5.366504683306542 -5.8457948614263024 7.117346683117635 2.4719309431084096 -10.9878149309132 6.206666666290314 -4.81355283878034 2.556481864248628 1.544607529026366 0.32771719963811274 -8.347194008599761 -11.8841639324856 0.0783224610589292 4.734256868586167 -5.0586763297713535 1.0247243033606428 2.71570126073173 0.9887901698910944 9.023420847965944 5.474188338073132 -2.9483436105022633 0.6301843990004704 4.953143907421322 0.34586533024462857 6.12791261540209 9.297863647271994 -2.824933933216417 0.45356022554437225 -2.9121584307308854 3.494636465801179 2.3436752314569347 -3.5310664969990606 2.3267975329007133 -6.040330366384742 3.285445372480659 -9.834874616713016 6.77555596751939 3.7032153754816948 -5.5025924341393075 9.59413402057828 -0.5094859048631646 -6.061043638283955 -2.6728044936237616 -3.391619666421211 3.240137601640589 -0.01842350743728599 -3.51012386998522 2.4967993822606585 -11.078578060185206 taxon_14 1.073353760505365 5.5734767990134735 -2.6843066156558515 5.677935472306026 -2.699643233128126 -2.728007905793043 -0.392790446305412 2.6458388804094986 -1.3060865093811895 -1.7520250611103338 0.1575923757219606 -0.8077917459859683 -3.9200291928398183 6.27052847533536 -0.32977023164093744 -0.3712239781314066 -1.7577272515336166 -0.5884619750569766 -0.5957274215226168 -0.3593748972020159 4.0348907086606 -2.7033121473612303 -3.4139018429061174 4.551128612056906 -1.4239836999966955 -1.1578263312984811 -2.252529504672524 -5.667165010823732 2.8634347862273777 -3.682652763630837 2.827268502641909 0.7567651620959162 -0.7869646378499152 -4.995396780565182 -0.745931283541611 5.835555838446897 3.737265633497629 -2.166996339778634 -3.2706002507277634 -2.6804968423093065 9.25930419097416 2.1448931513859235 1.2537695313470443 1.4939077817282298 -1.5130532738248923 1.4191687093887406 -1.456817347584686 -1.339229194021417 -0.09394674573952344 -2.2640810134164884 taxon_15 -12.444465554325378 4.836625200513874 -2.2657018000555906 5.28275932092579 -3.0404718381934486 -7.643380653321292 8.150185373958202 -4.598657218930686 -0.7608563739597207 -2.918546721420061 -1.7231515608650922 -3.403627855882959 -6.029797738139418 1.2895373765695695 2.08574412638709 -4.381707660719245 -2.222864063494854 1.648798837291138 0.13256620707433586 7.562033262921517 -0.5521287547663918 2.2010800670211257 -4.129730887884562 8.013380743209533 -2.8655472264901 5.229291691235364 9.108188453826383 -1.4219751759085024 1.1870846372560537 -4.671190081001982 6.127888778567955 3.642641381528749 -11.38851597825588 1.9397988079427542 -4.47185464188104 7.5380191906373675 -1.7769042119882306 6.334182727041377 1.39891725462765 -0.5325219918233925 2.8260268065582363 -6.534326212570642 -3.8899161705975134 -2.282362853558323 -6.499338595082964 8.273586276707144 -2.764740091846174 -1.730886586775291 0.15535847328174937 -9.454273481857522 ; BLOCKID WM114cbdd48540; END; BEGIN TREES; Title 'Trees from "09-pcaSim.nex"'; LINK Taxa = Untitled_Block_of_Taxa; TRANSLATE 1 taxon_0, 2 taxon_1, 3 taxon_2, 4 taxon_3, 5 taxon_4, 6 taxon_5, 7 taxon_6, 8 taxon_7, 9 taxon_8, 10 taxon_9, 11 taxon_10, 12 taxon_11, 13 taxon_12, 14 taxon_13, 15 taxon_14, 16 taxon_15; TREE species_phylogeny = (((1:5.83,(11:8.833[%color = 5 ],(((7:2.0,12:1.778):1.857,15:1.857):3.2,(6:9.0[%color = 11 ],((8:4.0,14:3.5):4.0,(16:2.8,5:1.636):3.25):3.0):8.0):1.6):1.7):1.538,3:8.571[%color = 6 ]):1.857,(13:6.0,(((4:4.0,10:2.25):2.0,9:2.143):2.2,2:4.333):4.5):7.5):2.0; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = Squared: 1 - 50; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = Brownian_default: 1 - 50; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 662863783909563173 WM114cbdd482a17; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 2885845513937770954 WM114cbdd48540; checksum 0 284355860 WM114cbdd48540; endTell; getWindow; tell It; setResourcesState false true 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 435 268; setLocation 2 31; setFont SanSerif; setFontSize 10; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #662863783909563173 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 2151.964555237631.1796649727975159086; getTreeWindow; tell It; popAsTile false; popOut; setExplanationSize 20; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 533 293; setLocation 447 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; stretchToggle off; branchLengthsToggle on; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 8; orientUp; toggleCorners off; endTell; setBackground White; setBranchColor Black; showNodeNumbers off; showBranchColors on; labelBranchLengths off; centerBrLenLabels on; showBrLensUnspecified on; showBrLenLabelsOnTerminals on; setBrLenLabelColor 0 0 255; setNumBrLenDecimals 6; desuppress; getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames; tell It; setFont SanSerif; setFontSize 10; setColor Black; toggleColorPartition on; toggleShadePartition off; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; useSuggestedSize off; toggleSizeToFit on; toggleTextOnTree off; showWindow; endTell; getEmployee #mesquite.trees.ColorBranches.ColorBranches; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.ornamental.BranchNotes.BranchNotes; tell It; setAlwaysOn off; endTell; getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition; tell It; colorByPartition off; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; makeTreeWindow #662863783909563173 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 2169.964555238096.1130981136534120104; getTreeWindow; tell It; popAsTile false; popOut; setExplanationSize 20; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 533 362; setLocation 453 437; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.cont.PlotTree.PlotTree; tell It; setNodeLocs #mesquite.cont.NodeLocs2DPlot.NodeLocs2DPlot; tell It; hide; setAxis #mesquite.cont.MapContinuous.MapContinuous; tell It; getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed; tell It; setCharacterSource #mesquite.rhetenor.CharFromOrdinations.CharFromOrdinations; tell It; getCharacterSource #mesquite.charMatrices.CharMatrixCoordIndep.CharMatrixCoordIndep; tell It; setCharacterSource #mesquite.charMatrices.StoredMatrices.StoredMatrices; tell It; setDataSet #2885845513937770954; endTell; endTell; setOrdinator #mesquite.rhetenor.PrincipalComponents.PrincipalComponents; setItem 0; endTell; endTell; setCharacter 2; setItem 0; getEmployee #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates; tell It; setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels; tell It; setDefaultModel 13; endTell; toggleMPRsMode off; getEmployee #mesquite.parsimony.ParsimonySquared.ParsimonySquared; tell It; toggleWeight on; endTell; endTell; endTell; toggleShowLegend on; setInitialOffsetX -253; setInitialOffsetY -129; setCurrentX 1; setCurrentY 2; show; endTell; setSpotDiameter 10; toggleShowTerminals on; toggleShowInternals on; toggleShowTree on; endTell; setBackground White; setBranchColor Black; showNodeNumbers off; showBranchColors on; labelBranchLengths off; centerBrLenLabels on; showBrLensUnspecified on; showBrLenLabelsOnTerminals on; setBrLenLabelColor 0 0 255; setNumBrLenDecimals 6; desuppress; getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames; tell It; setFont SanSerif; setFontSize 10; setColor Black; toggleColorPartition on; toggleShadePartition off; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; useSuggestedSize off; toggleSizeToFit on; toggleTextOnTree off; showWindow; endTell; getEmployee #mesquite.trees.ColorBranches.ColorBranches; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.ornamental.BranchNotes.BranchNotes; tell It; setAlwaysOn off; endTell; getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition; tell It; colorByPartition off; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #2885845513937770954 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; popAsTile false; popOut; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 427 327; setLocation 4 384; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleShowChanges on; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames on; toggleShowDefaultCharNames off; toggleConstrainCW on; setColumnWidth 70; toggleBirdsEye off; toggleAllowAutosize on; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel; tell It; togglePanel off; endTell; getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; endTell; endTell; newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator; tell It; setNextFileName '10-pcaLiveSim.nex'; setPrevFileName '08-anoles.nex'; getWindow; tell It; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 435 251; setLocation 2 31; setFont SanSerif; setFontSize 10; setActive; setExplanation 'The tree at right was used to simulate evolution by Brownian motion to yield the data matrix shown below. The same tree is plotted in PCA space calculated from the simulated characters, lower right. Notice that the different clades stand out clearly on the plot.^n'; setTitle Simulated_data; toggleFileNames off; setPrevButtonName Previous; setNextButtonName Next; endTell; showWindow; endTell; endTell; end;