Unable to import tree

[marco iocchi]

Hi everyone,

I tried to import a phylogenetic tree (.tre format file) using the 3.1 version but the program says that is unable to import the tree.

The strange thing is that the same .tre file works in 1.1 version an works well also in FigTree

I'm using Biodiverse on a WINDOWS OS

The following is the newick text of the .tre file:

(((((((((((((((Polystichum_x_bicknellii:6,Polystichum_setiferum:6.000000,Polystichum_lonchitis:6.000000,Polystichum_aculeatum:6.000000)Polystichum:65.000000,(Dryopteris_pallida:35.9,(Dryopteris_villarii:17.950001)N210:17.950001,((Dryopteris_filix-mas:1.000000,Dryopteris_affinis:1.000000)Dryopteris_filix-mas_agg.:26.000000)N213:8.900002)Dryopteris:35.099998)Dryopteridaceae:22.599998,(((((Polypodium_interjectum:21.950001,Polypodium_vulgare:21.950001,Polypodium_cambricum:21.950001)Polypodiaceae:21.950001)N239:3.769997)N237:15.310001)N235:15.310001)N233:15.310000)Eupolypods_I:11.099998,((((Asplenium_balearicum:39.168,Asplenium_ceterach:39.168,Asplenium_lepidum:39.168,Asplenium_obovatum:39.168,Asplenium_petrarchae:39.168,Asplenium_sagittatum:39.168,Asplenium_scolopendrium:39.168,Asplenium_x_tyrrhenicum:39.168)Asplenium:39.168,((Asplenium_ruta-muraria:26.112000)N155:26.112000,(Asplenium_adiantum-nigrum:26.112000,Asplenium_onopteris:26.112000)N158:26.112000)N154:26.112000,(((((Asplenium_septentrionale:14.028000)N173:14.028000)N169:14.028000,(Asplenium_viride:30.000000,Asplenium_trichomanes:30.000000)N177:12.084000)N168:12.084000,(Asplenium_fissum:27.084000,Asplenium_marinum:27.084000)N181:27.084000)N167:12.084000)N163:12.084000)Aspleniaceae:12.084000,(((Thelypteris_palustris:28.779999)N186:28.779999)Thelypteridaceae:28.779999,(((Blechnum_spicant:74.099998)N196:4.080002,(Athyrium_filix-femina:52.119999,(Athyrium_distentifolium:26.059999)N204:26.059999)Athyrium:26.060001)N195:4.080002)N190:4.079994)N184:4.080002)N152:4.080000,(((Cystopteris_fragilis:28.699999,Cystopteris_alpina:28.699999)Cystopteris_fragilis_agg.:28.699999)Cystopteris:28.699999,(Gymnocarpium_robertianum:43.049999,Gymnocarpium_dryopteris:43.049999)Gymnocarpium:43.049999)N140:8.400002)Eupolypods_II:10.199997)Eupolypods:39.800003,((Oeosporangium_acrosticum:48.705)Oeosporangium:48.705,(((Pteris_cretica:30.666666)Pteris:30.666666,Anogramma_leptophylla:61.333332)N128:30.666666,(Adiantum_capillus-veneris:73.730003)N133:18.269997)N127:5.410004)Pteridaceae:47.089996,Pteridium_aquilinum:144.500000)N123:31.300003)Polypodiales:35.000000)N105:9.199997,(((Salvinia_natans:44.500000)Salvinia:44.500000)Salviniaceae:84.300003)Salviniales:46.699997)Core_Leptosporangiates:46.299988)N87:19.900024)N75:36.899994,Osmunda_regalis:323.100006)Leptosporangiatae:36.500000,(((Equisetum_variegatum:19.200001,(Equisetum_ramosissimum:13.000000,Equisetum_hyemale:13.000000,Equisetum_x_moorei:13.000000)N53:6.200001)Hypochaete:73.250000,((Equisetum_telmateia:15.700001,(Equisetum_palustre:12.700001,((Equisetum_fluviatile:6.700000,Equisetum_arvense:6.700000)N67:3.000000)N65:3.000001)N63:3.000000)N61:3.000000)Equisetum:73.750000)Equisetaceae:261.549988)N49:5.600006)N48:4.799988,((((Botrychium_lunaria:5.000000)N36:52.799999)Botrychium:104.199997,(Ophioglossum_vulgatum:81.000000,Ophioglossum_azoricum:81.000000,Ophioglossum_lusitanicum:81.000000)Ophioglossum:81.000000)Ophioglossaceae:143.600006)Psilotopsida:58.799988)Pteridophyta:48.700012)Crown_euphyllophytes:12.399994,(Huperzia_selago:384.100000,(Selaginella_denticulata:359.460000,(Isoetes_longissima:347.160000,(Isoetes_histrix:344.160000,(Isoetes_sabatina:342.160000,Isoetes_durieui:342.160000)N1000:2.000000)N1001:3.000000)Isoetales:12.300000)Selaginellales:24.640000)Lycopodiales:41.650000)Vascular_plants:1.000000[NOTE: 1 taxon not matched: notmatched/genx/Genx_spy, ];

Someone can help me with this issue

thanks 

[marco iocchi]

Hi everyone,

I've been lucky... I tried removing this part of the text: ...[NOTE: 1 taxon not matched: notmatched/genx/Genx_spy, ]... within the .tre file an now it's working

the tree has been imported succesfully

best regards

[Shawn Laffan]

Hello Marco,

Thanks for reporting this.  I've raised an issue so it will be fixed for the next version:  https://github.com/shawnlaffan/biodiverse/issues/758

Deleting the trailing comment from the tree file, as you have done, will get things working in the meantime.

Regards,
Shawn.

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