[phylocom-user] Adding age using bladj and Wikstrom age file

Wuu Kuang Soh wuukuang at gmail.com
Thu May 7 01:33:35 PDT 2015


Hi folks,

I have a Phylocom question to ask you, I have read the manual and went
through the archives but could not find a solution. I got this tree using
Phylomatic (see attached) and I want to add the age using Wikstrom age file
using bladj (I'm using Window 7). Some how fail to do so, with error
message saying Phylocom.exe failed. I have also went through online
tutorial etc. but still in vain. I did notice that in bladj instruction it
says that 'IMPORTANT: the root node of the phylogeny must be named and
given an age.'. But I'm not sure if I did this or not.

If it is a matter of the software problem, is there any other way of
putting this age on my tree. Can I manually type in the age into the newick
file.

Many thanks,
Wuu Kuang

Post-doctoral researcher,

Plant Palaeoecology and Palaeobiology Group

Room E4.51, Earth Institute, Science East,

School of Biology and Environmental Science,

University College Dublin,

Belfield, Dublin 4, Ireland.

http://www.ucd.ie/plantpalaeo/soh.html
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(((((((((((((acacia_constricta,acacia_greggii)acacia,(calliandra_eriophylla,pithecellobium_unguis-cati)),prosopis_velutina),((andira_inermis,pictetia_aculeata),lupinus_arboreus)),(cercidium_floridum,cercidium_microphyllum)cercidium)fabaceae,((((((adenostoma_fasciculatum,((((amelanchier_arborea,amelanchier_utahensis)amelanchier,crataegus_mollis),((cotoneaster_coriaceus,cotoneaster_pannosus)cotoneaster,malus_fusca),heteromeles_arbutifolia,(sorbus_scopulina,sorbus_sp.)sorbus)pyrinae,(holodiscus_discolor,(spiraea_beauverdiana,spiraea_douglasii,spiraea_latifolia)spiraea)spiraeeae),oemleria_cerasiformis),(prunus_emarginata,prunus_ilicifolia,prunus_serotina,prunus_sp)prunus),cercocarpus_betuloides),amelanchier_alnifolia,potentilla_fruticosa,(rosa_acicularis,rosa_gymnocarpa,rosa_nutkana)rosa,(rubus_idaeus,rubus_parviflorus,rubus_praecox,rubus_spectabilis,rubus_ursinus)rubus,sphaeralcea_taxa)rosaceae,(((((ceanothus_cuneatus,ceanothus_oliganthus,ceanothus_thyrsiflorus)ceanothus,colubrina_elliptica,(ziziphus_obtusifolia,ziziphus_reticulata)ziziphus)ziziphoids,((reynosia_uncinata,krugiodendron_ferreum)rhamneae,(rhamnus_californica,rhamnus_crocea,rhamnus_purshiana)rhamnus))rhamnaceae,shepherdia_canadensis),(((celtis_laevigata,celtis_pallida)celtis,pseudolmedia_spuria),ulmus_americana)))rosales,((((((alnus_rhombifolia,alnus_rubra,alnus_serrulata,alnus_viridis,alnus_incana)alnus,(betula_kenaica,betula_nana,betula_neoalaskana,betula_populifolia,betula_alleghaniensis)betula)betuloideae,((carpinus_caroliana,ostrya_virginiana),corylus_cornuta)coryloideae),(carya_ovata,(myrica_californica,comptonia_peregrina)myricaceae)),((quercus_agrifolia,quercus_alba,quercus_falcata,quercus_lobata,quercus_michauxii,quercus_palustris,quercus_rubra,quercus_tubirnella)quercus,fagus_grandifolia)fagaceae),marah_oreganus))),((calophyllum_brasiliense,((casearia_decandra,casearia_guianensis,casearia_sylvestris,tetrazygia_eleagnoides)casearia,(populus_balsamifera,populus_fremontii,populus_tremuloides)populus,(salix_alaxensis,salix_barclayi,salix_exigua,salix_gooddingii,salix_hookeriana,salix_lasiandra,salix_lasiolepis,salix_nigra,salix_scouleriana,salix_sitchensis,salix_sp1,salix_sp2,salix_sp3)salix)salicaceae,((croton_betulinus,croton_discolor,croton_humilis)croton,gymnanthes_lucida)euphorbiaceae,drypetes_alba,(erythroxylum_areolatum,erythroxylum_rotundifolium)erythroxylum,malpighia_coccigera)malpighiales,(cassine_xylocarpa,(schaefferia_frutescens,schefflera_morototoni)schaefferia,crossopetalum_rhacoma,euonymus_americanus,gyminda_latifolia)celastraceae)celastrales_to_malpighiales),(guaiacum_officinale,larrea_tridentata)zygophyllaceae)fabids,(((((((acer_macrophyllum,acer_negundo,acer_pensylvanicum,acer_rubrum,acer_saccharum,acer_spicatum)acer,aesculus_californica,allophylus_crassinervis,cupania_americana,dodonaea_viscosa,hypelate_trifoliata,thouinia_striata)sapindaceae,((swietenia_macrophylla,swietenia_mahogani)swietenia,zanthoxylum_flavum)),(comocladia_glabra,rhus_copallinum_,toxicodendron_diversilobum)anacardiaceae),((capparis_cynophallophora,capparis_flexuosa,capparis_indica)capparis,(dirca_occidentalis,(helicteres_jamaicensis,tilia_americana)malvaceae))malvales_to_brassicales),picramnia_pentandra),(bucida_buceras,(miconia_prasina,(psidium_amplexicaule,(eugenia_axillaris,eugenia_biflora,eugenia_ligustrina,eugenia_rhombea)eugenia)))myrtales)malvids),((ribes_hudsonianum,ribes_laxiflorum,ribes_sanguineum,ribes_sp,ribes_triste,rosa_californica)ribes,(hamamelis_virginiana,liquidambar_styraciflua))),(((((((((ambrosia_ambrosioides,eriophyllum_stoechadifolium),artemisia_carruthii),(baccharis_pilularis,baccharis_salicifolia,baccharis_sarothroides)baccharis,encelia_farinosa,gutierrezia_sarothrae)asteraceae,(oplopanax_horridus,(((sambucus_canadensis,sambucus_nigra,sambucus_racemosa)sambucus,(viburnum_acerifolium,viburnum_edule,viburnum_prunifolium,viburnum_recognitum)viburnum)adoxaceae,(linnaea_borealis,(lonicera_hispidula,lonicera_involucrata,lonicera_morrowii)lonicera,symphoricarpos_albus)caprifoliaceae)dipsacales)),(ilex_opaca,ilex_verticillata)ilex)campanulids,(((((((((antirhea_lucida,guettarda_elliptica),gonzalagunia_hirsuta),rondeletia_inermis),erithalis_fruticosa)cinchonoideae,randia_aculeata),neolaugeria_resinosa,psychotria_nervosa,faramea_occidentalis)rubiaceae,plumeria_alba)gentianales,((((mimulus_aurantiacus,lepechinia_calycina),chilopsis_linearis),(chionanthus_holdridgii,(fraxinus_pennsylvanica,fraxinus_velutina)fraxinus)oleaceae),lycium_fremontii),(rochefortia_acanthophora,eriodictyon_californicum)boraginaceae),garrya_elliptica)lamiids),((((arbutus_menziesii,(arctostaphylos_columbiana,arctostaphylos_uva-ursi)arctostaphylos,menziesia_ferruginea,(rhodendron_macrophyllum,rhodendron_occidentale)rhodendron,rhododendron_maximum,gaultheria_shallon,kalmia_latifolia,(vaccinium_angustifolium,vaccinium_corymbosum,vaccinium_ovatum,vaccinium_parviflorum,vaccinium_vitis-idaea)vaccinium)ericaceae,cyrilla_racemiflora),((ardisia_obovata,diospyros_virginiana),chrysophyllum_oliviforme)),fouquieria_splendens))ericales_to_asterales,(nyssa_slyvatica,(cornus_amomum,cornus_florida,cornus_sericea,cornus_sp.)cornus)cornaceae)asterids,(((neea_buxifolia,guapira_obtusata)nyctaginaceae,simmondsia_chinensis),(coccoloba_diversifolia,(eriogonum_fasciculatum,eriogonum_latifolium)eriogonum)polygonaceae)caryophyllales)),(berberis_aquifolium,berberis_nervosa,berberis_thunbergii)berberis)eudicots,(((asimina_triloba,liriodendron_tulipifera),(nectandra_coriacea,(sassafras_albidum,sassafras_albidum_)sassafras,licaria_parvifolia,lindera_benzoin,umbellularia_californica)lauraceae),canella_winterana)magnoliids)magnoliales_to_asterales;


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