Created a copy of the tree and character files for the Heliconia dataset...

anolis/README.md

@@ -20,4 +20,6 @@ Analysis "Anolis B"
 3. Match the row names in the matrix to the tips of the tree
 4. Reconstruct ancestral states for ecomorph and make a plot.
 
-Comparing the results of these two workflows will give some insight into how well we can do by pulling from openTree.
+Comparing the results of these two workflows will give some insight into how well we can do by pulling from openTree.
+
+Added anolis_fullnames.phy to match the names in anolis_fullnames.csv and be useful when query third party services (full scientific names).

anolis/anolis_fullnames.phy

@@ -0,0 +1 @@
+((((((((Anolis_ahli:0.1308887296,Anolis_allogus:0.1308887296):0.109078899,Anolis_rubribarbus:0.2399676286):0.3477240729,Anolis_imias:0.5876917015):0.1279779191,((((Anolis_sagrei:0.2576204042,(Anolis_bremeri:0.1097436524,Anolis_quadriocellifer:0.1097436524):0.1478767518):0.06150599843,Anolis_ophiolepis:0.3191264027):0.08721921759,Anolis_mestrei:0.4063456203):0.1298140501,(((Anolis_jubar:0.1188659524,Anolis_homolechis:0.1188659524):0.09052271908,Anolis_confusus:0.2093886715):0.04215577182,Anolis_guafe:0.2515444433):0.2846152271):0.1795099503):0.1377237125,((((Anolis_garmani:0.2000335809,Anolis_opalinus:0.2000335809):0.01968719882,Anolis_grahami:0.2197207797):0.2178099139,Anolis_valencienni:0.4375306936):0.1226128606,(Anolis_lineatopus:0.4713710622,Anolis_reconditus:0.4713710622):0.08877249208):0.2932497789):0.06703519523,(((Anolis_evermanni:0.2135202715,Anolis_stratulus:0.2135202715):0.3521520586,(((Anolis_krugi:0.3267560653,Anolis_pulchellus:0.3267560653):0.1312930371,(Anolis_gundlachi:0.3864660126,Anolis_poncensis:0.3864660126):0.0715830898):0.03035078065,(Anolis_cooki:0.395288192,Anolis_cristatellus:0.395288192):0.09311169105):0.07727244709):0.1495575755,(((Anolis_brevirostris:0.2757423466,(Anolis_caudalis:0.1704974619,Anolis_marron:0.1704974619):0.1052448847):0.02672749452,Anolis_websteri:0.3024698411):0.09835748687,Anolis_distichus:0.400827328):0.3144025776):0.2051986227):0.03488732303,(((Anolis_barbouri:0.8021085018,(((Anolis_alumina:0.2681076879,Anolis_semilineatus:0.2681076879):0.219367178,Anolis_olssoni:0.4874748658):0.2622236606,(Anolis_etheridgei:0.5883072151,(Anolis_fowleri:0.3770938401,Anolis_insolitus:0.3770938401):0.211213375):0.1613913113):0.05240997539):0.0672038969,((((Anolis_whitemani:0.3420271265,((Anolis_haetianus:0.2669834072,Anolis_breslini:0.2669834072):0.06962183477,((Anolis_armouri:0.1483909526,Anolis_cybotes:0.1483909526):0.04416718222,Anolis_shrevei:0.1925581348):0.1440471072):0.005421884492):0.1066560095,(Anolis_longitibialis:0.2521253346,Anolis_strahmi:0.2521253346):0.1965578014):0.09143002532,Anolis_marcanoi:0.5401131613):0.2505275207,((((((Anolis_baleatus:0.04173045424,Anolis_barahonae:0.04173045424):0.05263675531,Anolis_ricordii:0.09436720956):0.2036021511,Anolis_eugenegrahami:0.2979693606):0.0851110199,Anolis_christophei:0.3830803805):0.09095334022,Anolis_cuvieri:0.4740337207):0.1076385501,(Anolis_barbatus:0.1467942669,(Anolis_porcus:0.09310584235,(Anolis_chamaeleonides:0.07630236186,Anolis_guamuhaya:0.07630236186):0.01680348049):0.05368842459):0.4348780039):0.2089684112):0.07867171672):0.07597999248,((((((((Anolis_altitudinalis:0.1748899419,Anolis_oporinus:0.1748899419):0.09220318062,Anolis_isolepis:0.2670931225):0.2538920892,(Anolis_allisoni:0.29602293,Anolis_porcatus:0.29602293):0.2249622817):0.03703491197,(((Anolis_argillaceus:0.1142165228,Anolis_centralis:0.1142165228):0.0249762444,Anolis_pumilis:0.1391927672):0.2356256274,Anolis_loysiana:0.3748183946):0.1832017291):0.08522862529,Anolis_guazuma:0.6432487489):0.04644117492,((Anolis_placidus:0.1869579579,Anolis_sheplani:0.1869579579):0.3773659809,(Anolis_alayoni:0.3793818065,(Anolis_angusticeps:0.2172126961,Anolis_paternus:0.2172126961):0.1621691104):0.1849421323):0.125365985):0.07887044542,((Anolis_alutaceus:0.120861969,Anolis_inexpectatus:0.120861969):0.4042515809,(((Anolis_clivicola:0.3359598029,(Anolis_cupeyalensis:0.08606303065,Anolis_cyanopleurus:0.08606303065):0.2498967723):0.1189736423,(Anolis_alfaroi:0.2802339379,Anolis_macilentus:0.2802339379):0.1746995073):0.0092278683,Anolis_vanidicus:0.4641613135):0.06095223642):0.2434468193):0.09435314761,(Anolis_argenteolus:0.6564331946,Anolis_lucius:0.6564331946):0.2064803223):0.08237887432):0.01002346021):0.04468414858,(((Anolis_bartschi:0.5247253674,Anolis_vermiculatus:0.5247253674):0.249459768,((((Anolis_baracoae:0.05853977536,(Anolis_noblei:0.02140617522,Anolis_smallwoodi:0.02140617522):0.03713360014):0.02849164237,Anolis_luteogularis:0.08703141773):0.017899207,Anolis_equestris:0.1049306247):0.6297194497,(((Anolis_monticola:0.6055537678,(Anolis_bahorucoensis:0.3841100683,(Anolis_dolichocephalus:0.1509270933,Anolis_hendersoni:0.1509270933):0.2331829749):0.2214436996):0.03149201716,Anolis_darlingtoni:0.637045785):0.03288736013,(((Anolis_aliniger:0.1783542747,Anolis_singularis:0.1783542747):0.1377057507,Anolis_chlorocyanus:0.3160600254):0.2135626601,Anolis_coelestinus:0.5296226856):0.1403104596):0.0647169293):0.0395350609):0.1207482386,Anolis_occultus:0.8949333739):0.1050666261);

heliconia/HeliconiaReadMe.md

@@ -25,3 +25,5 @@ Analysis "Heliconia B"
 5. phylogenetic signal of all traits individually
 
 These analyses will test the use of potential source trees with branch lenghts from OpenTree in Arbor to be used in comparative methods
+
+Files HeliconiaSelectEditFullname.phy and heliconiaFullname.csv have been edited to use full scientific name to facilitate searching in other taxonomic services.

heliconia/HeliconiaSelectEditFullname.phy

@@ -0,0 +1 @@
+(((((((((Heliconia_abaloi:4.19894,Heliconia_pastazae:4.19894):3.1876,Heliconia_paludigena:7.38655):2.87423,((((Heliconia_arrecta:2.63237,Heliconia_mucilagina:2.63237):1.22189,Heliconia_spiralis:3.85425):5.62104,Heliconia_venusta:9.4753):0.458336,((Heliconia_chartacea:7.1706,(Heliconia_peteriana:5.28305,Heliconia_vellerigera:5.28305):1.88755):1.70932,((Heliconia_episcopalis:6.16766,Heliconia_marginata:6.16766):1.67246,((Heliconia_plowmaniana:5.29612,Heliconia_waoraniana:5.29612):1.55309,Heliconia_rostrata:6.84921):0.990914):1.03979):1.05372):0.327142):0.684813,(Heliconia_aemygdiana:7.75523,Heliconia_pseudoaemygdiana:7.75523):3.19036):0.974862,Heliconia_berryi:11.9205):2.26971,((((((((Heliconia_aurea:4.82091,Heliconia_rodriguensis:4.82091):0.964295,(((Heliconia_lennartiana:2.06863,Heliconia_nitida:2.06863):1.73877,Heliconia_wagneriana:3.80741):1.01788,Heliconia_stricta:4.82529):0.959916):0.643073,((Heliconia_caribaea:1.71176,Heliconia_monteverdensis:1.71176):1.1308,Heliconia_undulata:2.84256):3.58572):1.33403,Heliconia_bihai:7.76231):2.21671,(Heliconia_pendula:7.77078,Heliconia_villosa:7.77078):2.20824):1.6404,(Heliconia_julianii:6.61984,Heliconia_velutina:6.61984):4.99958):0.600798,((((((Heliconia_deflexaP:2.48575,Heliconia_mathiasiae:2.48575):2.361,Heliconia_wilsonii:4.84675):0.524526,Heliconia_metallica:5.37128):1.09871,Heliconia_osaensis:6.46999):1.27494,(Heliconia_golfodulcensis:4.66551,Heliconia_vaginalis:4.66551):3.07942):2.14027,(Heliconia_meridensis:5.875,Heliconia_mincana:5.875):4.0102):2.33501):1.22642,(((Heliconia_badilloi:5.09969,(Heliconia_lentiginosa:4.16931,((Heliconia_obscura:2.66665,(Heliconia_riopalenquensis:1.64068,Heliconia_sclerotricha:1.64068):1.02597):1.1919,Heliconia_obscuroides:3.85854):0.310766):0.930376):1.59082,((Heliconia_robertoi:4.84673,(((Heliconia_laxa:2.13203,Heliconia_lozanoi:2.13203):0.876468,Heliconia_oleosa:3.0085):0.652041,Heliconia_reptans:3.66054):1.18619):0.971542,Heliconia_robusta:5.81827):0.872232):1.12198,(((Heliconia_caquetensis:4.89744,Heliconia_dielsiana:4.89744):0.932005,Heliconia_huilensis:5.82944):1.25569,Heliconia_estiletioides:7.08513):0.727346):5.63416):0.743524):0.42256,(((((Heliconia_acuminata:5.59206,(Heliconia_brachyantha:4.39195,Heliconia_tarumaensis:4.39195):1.20011):1.36659,Heliconia_psittacorum:6.95864):1.48094,(Heliconia_densiflora:7.26599,Heliconia_timothei:7.26599):1.1736):0.637249,Heliconia_sylvestris:9.07683):1.88832,(Heliconia_dasyantha:6.31712,Heliconia_richardiana:6.31712):4.64803):3.64757):0.270526,((((((((((Heliconia_beckneri:1.56115,Heliconia_chrysocraspeda:1.56115):1.88252,Heliconia_umbrophila:3.44368):0.426249,Heliconia_latispatha:3.86992):1.33271,Heliconia_tortuosa:5.20264):1.59628,(Heliconia_atropurpurea:4.45054,Heliconia_bella:4.45054):2.34837):0.374047,(Heliconia_clinophila:5.04912,Heliconia_darienensis:5.04912):2.12385):0.871457,Heliconia_reticulata:8.04442):0.563885,(Heliconia_gracilis:3.32448,Heliconia_rodriguezii:3.32448):5.28382):1.61128,((Heliconia_bourgaeana:4.80436,Heliconia_librata:4.80436):3.5695,Heliconia_lophocarpa:8.37386):1.84573):2.18555,Heliconia_mooreana:12.4051):2.47811):11.6989,(Heliconia_brenneri:18.9784,(((Heliconia_gaiboriana:4.11882,Heliconia_willisiana:4.11882):0.906514,Heliconia_virginalis:5.02534):13.4501,((Heliconia_indica:5.8999,Heliconia_papuana:5.8999):4.24546,(((Heliconia_lanata:3.5467,Heliconia_solomonensis:3.5467):2.42033,Heliconia_paka:5.96703):1.67556,Heliconia_laufao:7.64259):2.50277):8.33009):0.502958):7.60374);