[phylocom-user] bladj segmentation fault

Thomas Kraft tsk29 at cornell.edu
Fri May 20 05:35:24 PDT 2011


Below I have included the taxa list data file (used in phylomatic) and the
output newick tree. The ages file that I am using is the wikstrom.ages that
comes in the example folder, so I would assume there are no problems with
it. It seems like a complete summary of the wikstrom et al. paper data. But
I'm still getting the segmentation fault error when I try to run it with
bladj. Thanks to all for the help!

Taxa:

sapotaceae/aningeria/aningeria_altissima
cornaceae/alangium/alangium_chinense
fabaceae/albizia/albizia_grandibracteata
moraceae/antiaris/antiaris_toxicaria
sapindaceae/aphania/aphania_senegalensis
zygophyllaceae/balanites/balanites_wilsonianus
euphorbiaceae/bridelia/bridelia_micrantha
salicaceae/casearia/casearia_battiscombei
rhizophoraceae/cassipourea/cassipourea_ruwensorensis
ulmaceae/celtis/celtis_africana
ulmaceae/celtis/celtis_durandii
ulmaceae/chaetacme/chaetacme_aristata
sapotaceae/chrysophyllum/chrysophyllum_albidum
rubiaceae/coffea/coffea_eugenioides
boraginaceae/cordia/cordia_abyssinica
ebenaceae/diospyros/diospyros_abyssinica
euphorbiaceae/drypetes/drypetes_battiscombei
moraceae/ficus/ficus_brachylepis
moraceae/ficus/ficus_exasperata
moraceae/ficus/ficus_natalensis
moraceae/ficus/ficus_vallis-choudae
bignoniaceae/kigelia/kigelia_africana
oleaceae/linociera/linociera_johnsonii
euphorbiaceae/macaranga/macaranga_schweinfurthii
primulaceae/maesa/maesa_lanceolata
fabaceae/milletia/milletia_dura
sapotaceae/mimusops/mimusops_bagshawei
oleaceae/olea/olea_capensis
salicaceae/oncoba/oncoba_spinosa
rubiaceae/oxyanthus/oxyanthus_speciosus
chrysobalanaceae/parinari/parinari_excelsa
pittosporaceae/pittosporum/pittosporum_mannii
apocynaceae/pleiocarpa/pleiocarpa_pycnantha
araliaceae/polyscias/polyscias_fulva
rosaceae/prunus/prunus_africana
anacardiaceae/pseudospondias/pseudospondias_microcarpa
apocynaceae/rauvolfia/rauvolfia_vomitoria
rubiaceae/rothmannia/rothmannia_urcelliformis
euphorbiaceae/sapium/sapium_ellipticum
olacaceae/strombosia/strombosia_scheffleri
clusiaceae/symphonia/symphonia_globulifera
rutaceae/teclea/teclea_nobilis
ulmaceae/trema/trema_orientalis
meliaceae/trichilia/trichilia_splendida
annonaceae/uvariopsis/uvariopsis_congensis
rubiaceae/vangueria/vangueria_apiculata


Newick output from phylomatic:

((((((((aningeria_altissima,chrysophyllum_albidum,mimusops_bagshawei)sapotaceae,(diospyros_abyssinica,maesa_lanceolata)),(((((coffea_eugenioides,vangueria_apiculata),oxyanthus_speciosus,rothmannia_urcelliformis)rubiaceae,(pleiocarpa_pycnantha,rauvolfia_vomitoria)apocynaceae)gentianales,cordia_abyssinica,(kigelia_africana,(linociera_johnsonii,olea_capensis)oleaceae)),(pittosporum_mannii,polyscias_fulva)))ericales_to_asterales,alangium_chinense)asterids,strombosia_scheffleri),(((((albizia_grandibracteata,milletia_dura)fabaceae,(((antiaris_toxicaria,(ficus_brachylepis,ficus_exasperata,ficus_natalensis,ficus_vallis-choudae)ficus),((celtis_africana,celtis_durandii)celtis,chaetacme_aristata,trema_orientalis)ulmaceae),prunus_africana)rosales),((bridelia_micrantha,drypetes_battiscombei,macaranga_schweinfurthii,sapium_ellipticum)euphorbiaceae,(casearia_battiscombei,oncoba_spinosa)salicaceae,cassipourea_ruwensorensis,parinari_excelsa,symphonia_globulifera)malpighiales),balanites_wilsonianus)fabids,((aphania_senegalensis,(teclea_nobilis,trichilia_splendida)),pseudospondias_microcarpa))),uvariopsis_congensis)magnoliales_to_asterales)euphyllophyte;



On Thu, May 19, 2011 at 6:05 PM, Scott Chamberlain
<myrmecocystus at gmail.com>wrote:

>  Could you provide the newick text and data file so we can perhaps
> reproduce the problem?
>
>
>
> Scott Chamberlain
> Rice University, EEB Dept.
>
> On Thursday, May 19, 2011 at 4:35 PM, Thomas Kraft wrote:
>
> Hello,
>
> I am currently attempting to build a tree with branch lengths for a very
> basic list of 46 angiosperm species. In the online phylomatic, I am able to
> generate a newick file with none of my species excluded. However, when
> attempting to use bladj in phylocom on the newick output from phylomatic, I
> receive the error "segmentation fault".  I have updated the ages file. Is
> there something else that I am missing, or is the online phylomatic not
> making the correct file format? Any help is greatly appreciated, thanks!
>
> Tom
> _______________________________________________
> phylocom-user mailing list
> phylocom-user at lists.phylodiversity.net
>
> http://lists.phylodiversity.net/listinfo.cgi/phylocom-user-phylodiversity.net
>
>
>
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