How can I obtain a phylogenetic tree for a subset of species?

[Alexander Ulrich]

For a recent manuscript the reviewers asked to present a phylogenetic tree the species that I have used for my analysis. This tree should contain exactly these species and give information about the temporal succession of splits. Since I am not an evolutionary biologist nor a bioinformatition I don't know if and how I could obtain such a tree.

Is there a possibility, for example a web tool, to select these exact species and just download the tree?

Thank you very much for your help!

-Alex-

[Joseph Brown]

Hi Alexander.

We have this service which will return a tree with a specified set of tips. It does not possess branch lengths (time or otherwise), so maybe it will not be of use to you? Note also that the tree will likely contain polytomies.

If you do want to pursue this, you need to provide identifiers ("ott_id"s) in the query. This service will allow you to find those ids from your species names.

If you have any trouble with this please do not hesitate to ask.

HTH.

Joseph.

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[Jonathan A Rees]

I think you want phylotastic (http://phylotastic.org/), which accesses the Open Tree tree.

Unfortunately their web portal http://phylo.cs.nmsu.edu:3000/ seems to be down right now, but I expect it will be back up again soon.

Jonathan

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[Alexander Ulrich]

Hi Jonathan, 

Thanks for your fast reply! 

Do you know if the tree I would obtain from plylostatic.org would include time-based branch lengths?

Best,

Alex

On Monday, January 23, 2017 at 2:42:17 AM UTC+1, Jonathan Rees wrote:

I think you want phylotastic (http://phylotastic.org/), which accesses the Open Tree tree.

Unfortunately their web portal http://phylo.cs.nmsu.edu:3000/ seems to be down right now, but I expect it will be back up again soon.

Jonathan

On Sun, Jan 22, 2017 at 3:03 PM, Alexander Ulrich <alexande...@gmail.com> wrote:

For a recent manuscript the reviewers asked to present a phylogenetic tree the species that I have used for my analysis. This tree should contain exactly these species and give information about the temporal succession of splits. Since I am not an evolutionary biologist nor a bioinformatition I don't know if and how I could obtain such a tree.

Is there a possibility, for example a web tool, to select these exact species and just download the tree?

Thank you very much for your help!

-Alex-

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[Karen Cranston]

Phylotastic does not contain branch lengths (although they are working on that functionality as part of the grant). Depending on the size of the tree, you could search TimeTree  (timetree.org) for individual divergence times from other studies. So getting the tree + dates would be a two-part job: 1) get a phylogeny from opentree; 2) manually annotate the internal nodes with dates from timetree.

I'll also note that this is an odd request from your reviewer, since inferring a tree with divergence times is not a trivial task (and could likely be a wholly separate research study, depending on the size of the tree).

[Joseph Brown]

Alexander,

This site (part of TimeTree) has full time-calibrated trees. I do not know which group you are working on, but hopefully it is there and you can just delete the unneeded tips.

HTH.

JWB

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[Alexander Ulrich]

Hi Karen,

Thank you for your reply, TimeTree seems to be an option! So far I only figured out how to get the divergence time of a pair of species. Since I have about 300 species in my tree this would take a bit manually. I also found an option on the TimeTree page to upload a list of species "Build a Timetree". I am hopeful that this option would generate a time tree of all of my ca. 300 species at once with proper branch lengths (not sure if that would really be the result). So I tried to upload a text file of species names (one per line) and also of species IDs (one per line). But in both cases I got the error message "Node IDs not found for taxa names". 

Do you know the "Build a Timetree" function?

Thank you very much!

[Alexander Ulrich]

Hi Joseph,

Thanks for the reply! My analysis covers ca. 300 species from the entire eukaryotic spectrum. So I would need to download the largest tree and delete a lot of branches. Manually that would take a while I guess. I am using iTOL for tree visualization. I am not sure if there is a fast way to delete all the additional species.

[Jim Allman]

On Jan 23, 2017, at 11:10 AM, Alexander Ulrich <alexande...@gmail.com> wrote:
>
> So I tried to upload a text file of species names (one per line) and also of species IDs (one per line). But in both cases I got the error message "Node IDs not found for taxa names”.

Hm, odd that it doesn’t report the failing names. If it’s just one or two names failing, you should be able to isolate them by splitting your name list into chunks and testing them separately. Eventually you should be able to winnow down the “failing” list to just the problematic name(s).

=jimA=

Jim Allman
Interrobang Digital Media
http://www.ibang.com/
(919) 649-5760

[Joseph Brown]

With a little bit of scripting (say, in R) it will be possible to prune down your tree appropriately. If you are not able to pull this off you can send me the trees and names and I can do it for you.

JWB

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[Alexander Ulrich]

Hi Jim, thanks for your reply.

For test purposes I even tried a list with just one name ('Homo sapiens') and it also didn't work. Always the same error message "Node IDs not found for taxa names”. I tried .txt and .rtf as file format. 

-Alex-

[Alexander Ulrich]

Hi Joseph,

I just tried the TimeTree function again and it seems to work now! At least it recognized most of the species (2/3). I guess the problem was that my text file contained a font which TimeTree didn't recognize. 

-Alex-

[Alexander Ulrich]

Surprisingly still 110 of 326 species could not be recognized by TimeTree. It looks like some species are simply not included in the > 50,000 species tree that seems to be the bases of TimeTree.org. Other species are included in the >50,000 species tree but could still not be retrieved by the "Build a TimeTree" function (e.g. Yarrowia lipolytica) although the species can be found in the pairwise function. 

[Joseph Brown]

Hi again Alexander.

I was unable to match 137 of your taxa to the tree (even after swapping in replacement conspecific taxa; results below). I don't really know how to advize further... Maybe argue with the reviewers that it is an unreasonable request? Divergence time estimation is a nuanced, difficult, computationally demanding venture.

JWB

       name                                      matched                         
  [1,] "Acromyrmex_echinatior"                   "Acromyrmex_balzani"            
  [2,] "Acyrthosiphon_pisum"                     "Acyrthosiphon_pisum"           
  [3,] "Aedes_aegypti"                           "Aedes_aegypti"                 
  [4,] "Agaricus_bisporus_(H97)"                 NA                              
  [5,] "Agaricus_bisporus_var._burnettii"        NA                              
  [6,] "Ailuropoda_melanoleuca"                  "Ailuropoda_melanoleuca"        
  [7,] "Ajellomyces_capsulatus"                  "Ajellomyces_capsulatus"        
  [8,] "Allomyces_macrogynus"                    "Allomyces_macrogynus"          
  [9,] "Alternaria_brassicicola"                 "Alternaria_alternata"          
 [10,] "Amphimedon_queenslandica"                "Amphimedon_queenslandica"      
 [11,] "Anolis_carolinensis"                     "Anolis_carolinensis"           
 [12,] "Anopheles_darlingi"                      "Anopheles_darlingi"            
 [13,] "Anopheles_gambiae"                       "Anopheles_gambiae"             
 [14,] "Apis_mellifera"                          "Apis_mellifera"                
 [15,] "Aquifex_aeolicus"                        NA                              
 [16,] "Arabidopsis_thaliana"                    "Arabidopsis_thaliana"          
 [17,] "Arthrobotrys_oligospora"                 "Arthrobotrys_elegans"          
 [18,] "Arthroderma_gypseum"                     "Arthroderma_benhamiae"         
 [19,] "Ashbya_gossypii"                         NA                              
 [20,] "Aspergillus_carbonarius"                 NA                              
 [21,] "Aspergillus_clavatus"                    "Aspergillus_clavatus"          
 [22,] "Aspergillus_flavus"                      "Aspergillus_flavus"            
 [23,] "Aspergillus_fumigatus"                   "Aspergillus_fumigatus"         
 [24,] "Aspergillus_kawachii"                    NA                              
 [25,] "Aspergillus_nidulans"                    NA                              
 [26,] "Aspergillus_niger"                       "Aspergillus_niger"             
 [27,] "Aspergillus_oryzae"                      "Aspergillus_oryzae"            
 [28,] "Aspergillus_terreus"                     "Aspergillus_terreus"           
 [29,] "Atta_cephalotes"                         "Atta_cephalotes"               
 [30,] "Aureococcus_anophagefferens"             "Aureococcus_anophagefferens"   
 [31,] "Auricularia_delicata"                    "Auricularia_auricula-judae"    
 [32,] "Babesia_bovis"                           NA                              
 [33,] "Bacillus_subtilis"                       "Bacillus_atticus"              
 [34,] "Bacteroides_thetaiotaomicron"            NA                              
 [35,] "Batrachochytrium_dendrobatidis"          NA                              
 [36,] "Beauveria_bassiana"                      "Beauveria_caledonica"          
 [37,] "Blastocystis_hominis"                    NA                              
 [38,] "Blastomyces_dermatitidis"                NA                              
 [39,] "Bombyx_mori"                             NA                              
 [40,] "Bos_taurus"                              "Bos_taurus"                    
 [41,] "Botryotinia_fuckeliana"                  "Botryotinia_fuckeliana"        
 [42,] "Brachypodium_distachyon"                 "Brachypodium_distachyon"       
 [43,] "Bradyrhizobium_japonicum"                NA                              
 [44,] "Branchiostoma_floridae"                  "Branchiostoma_floridae"        
 [45,] "Brassica_rapa_subsp._pekinensis"         "Brassica_rapa"                 
 [46,] "Brugia_malayi"                           NA                              
 [47,] "Caenorhabditis_brenneri"                 "Caenorhabditis_brenneri"       
 [48,] "Caenorhabditis_briggsae"                 "Caenorhabditis_briggsae"       
 [49,] "Caenorhabditis_elegans"                  "Caenorhabditis_elegans"        
 [50,] "Caenorhabditis_japonica"                 "Caenorhabditis_japonica"       
 [51,] "Caenorhabditis_remanei"                  "Caenorhabditis_remanei"        
 [52,] "Callithrix_jacchus"                      "Callithrix_jacchus"            
 [53,] "Camponotus_floridanus"                   "Camponotus_ocreatus"           
 [54,] "Candida_albicans"                        "Candida_albicans"              
 [55,] "Candida_dubliniensis"                    NA                              
 [56,] "Candida_glabrata"                        "Candida_glabrata"              
 [57,] "Candida_parapsilosis"                    NA                              
 [58,] "Candida_tropicalis"                      NA                              
 [59,] "Canis_familiaris"                        "Canis_latrans"                 
 [60,] "Capsaspora_owczarzaki"                   "Capsaspora_owczarzaki"         
 [61,] "Cavia_porcellus"                         "Cavia_porcellus"               
 [62,] "Chaetomium_globosum"                     "Chaetomium_elatum"             
 [63,] "Chlamydia_trachomatis"                   NA                              
 [64,] "Chlamydomonas_reinhardtii"               "Chlamydomonas_reinhardtii"     
 [65,] "Chlorella_variabilis"                    "Chlorella_vulgaris"            
 [66,] "Chloroflexus_aurantiacus"                NA                              
 [67,] "Ciona_intestinalis"                      "Ciona_intestinalis"            
 [68,] "Ciona_savignyi"                          "Ciona_intestinalis"            
 [69,] "Clavispora_lusitaniae"                   NA                              
 [70,] "Clonorchis_sinensis"                     NA                              
 [71,] "Coccidioides_immitis"                    "Coccidioides_immitis"          
 [72,] "Coccidioides_posadasii"                  "Coccidioides_posadasii"        
 [73,] "Cochliobolus_heterostrophus"             NA                              
 [74,] "Colletotrichum_gloeosporioides"          "Colletotrichum_gloeosporioides"
 [75,] "Coprinopsis_cinerea"                     "Coprinopsis_pseudonivea"       
 [76,] "Cordyceps_militaris"                     "Cordyceps_militaris"           
 [77,] "Crassostrea_gigas"                       "Crassostrea_gigas"             
 [78,] "Cricetulus_griseus"                      "Cricetulus_griseus"            
 [79,] "Cryphonectria_parasitica"                NA                              
 [80,] "Cryptococcus_gattii"                     "Cryptococcus_gattii"           
 [81,] "Cryptococcus_neoformans"                 "Cryptococcus_neoformans"       
 [82,] "Cryptosporidium_hominis"                 NA                              
 [83,] "Cryptosporidium_parvum"                  NA                              
 [84,] "Culex_quinquefasciatus"                  "Culex_quinquefasciatus"        
 [85,] "Danaus_plexippus"                        "Danaus_plexippus"              
 [86,] "Danio_rerio"                             "Danio_rerio"                   
 [87,] "Daphnia_pulex"                           "Daphnia_laevis"                
 [88,] "Debaryomyces_hansenii"                   "Debaryomyces_hansenii"         
 [89,] "Deinococcus_radiodurans"                 NA                              
 [90,] "Dictyoglomus_turgidum"                   NA                              
 [91,] "Dictyostelium_discoideum"                "Dictyostelium_discoideum"      
 [92,] "Dictyostelium_purpureum"                 "Dictyostelium_discoideum"      
 [93,] "Drosophila_ananassae"                    "Drosophila_ananassae"          
 [94,] "Drosophila_grimshawi"                    "Drosophila_mulleri"            
 [95,] "Drosophila_melanogaster"                 "Drosophila_melanogaster"       
 [96,] "Drosophila_mojavensis"                   "Drosophila_mojavensis"         
 [97,] "Drosophila_pseudoobscura"                "Drosophila_pseudoobscura"      
 [98,] "Drosophila_virilis"                      "Drosophila_virilis"            
 [99,] "Drosophila_willistoni"                   "Drosophila_willistoni"         
[100,] "Ectocarpus_siliculosus"                  NA                              
[101,] "Edhazardia_aedis"                        NA                              
[102,] "Encephalitozoon_cuniculi"                NA                              
[103,] "Entamoeba_histolytica"                   "Entamoeba_histolytica"         
[104,] "Enterocytozoon_bieneusi"                 NA                              
[105,] "Equus_caballus"                          "Equus_caballus"                
[106,] "Eremothecium_cymbalariae"                "Eremothecium_gossypii"         
[107,] "Escherichia_coli"                        NA                              
[108,] "Exophiala_dermatitidis"                  "Exophiala_dermatitidis"        
[109,] "Felis_catus"                             "Felis_catus"                   
[110,] "Fibroporia_radiculosa"                   NA                              
[111,] "Fusarium_oxysporum"                      NA                              
[112,] "Fusarium_pseudograminearum"              NA                              
[113,] "Fusarium_verticillioides"                NA                              
[114,] "Fusobacterium_nucleatum"                 NA                              
[115,] "Gaeumannomyces_graminis_var._tritici"    NA                              
[116,] "Gallus_gallus"                           "Gallus_gallus"                 
[117,] "Gasterosteus_aculeatus"                  "Gasterosteus_aculeatus"        
[118,] "Geobacter_sulfurreducens"                NA                              
[119,] "Geomyces_destructans"                    NA                              
[120,] "Giardia_intestinalis"                    "Giardia_intestinalis"          
[121,] "Gibberella_zeae"                         NA                              
[122,] "Glarea_lozoyensis"                       NA                              
[123,] "Gloeobacter_violaceus"                   NA                              
[124,] "Glycine_max"                             "Glycine_max"                   
[125,] "Gorilla_gorilla"                         "Gorilla_gorilla"               
[126,] "Grosmannia_clavigera"                    "Grosmannia_europhioides"       
[127,] "Halobacterium_salinarum"                 NA                              
[128,] "Harpegnathos_saltator"                   NA                              
[129,] "Heterobasidion_annosum"                  "Heterobasidion_parviporum"     
[130,] "Heterocephalus_glaber"                   "Heterocephalus_glaber"         
[131,] "Homo_sapiens"                            "Homo_sapiens"                  
[132,] "Hordeum_vulgare_var._distichum"          "Hordeum_pusillum"              
[133,] "Hyaloperonospora_arabidopsidis"          NA                              
[134,] "Hypocrea_virens"                         "Hypocrea_rufa"                 
[135,] "Ichthyophthirius_multifiliis"            NA                              
[136,] "Ixodes_scapularis"                       "Ixodes_uriae"                  
[137,] "Kazachstania_africana"                   NA                              
[138,] "Kluyveromyces_lactis"                    "Kluyveromyces_lactis"          
[139,] "Kluyveromyces_waltii"                    "Kluyveromyces_lactis"          
[140,] "Korarchaeum_cryptofilum"                 NA                              
[141,] "Laccaria_bicolor"                        "Laccaria_bicolor"              
[142,] "Lachancea_thermotolerans"                "Lachancea_kluyveri"            
[143,] "Latimeria_chalumnae"                     "Latimeria_chalumnae"           
[144,] "Leishmania_braziliensis"                 "Leishmania_infantum"           
[145,] "Leishmania_infantum"                     "Leishmania_infantum"           
[146,] "Leishmania_major"                        "Leishmania_major"              
[147,] "Leptosphaeria_maculans"                  "Leptosphaeria_maculans"        
[148,] "Leptospira_interrogans"                  NA                              
[149,] "Loa_loa"                                 "Loasa_filicifolia"             
[150,] "Lodderomyces_elongisporus"               NA                              
[151,] "Loxodonta_africana"                      "Loxodonta_africana"            
[152,] "Macaca_mulatta"                          "Macaca_mulatta"                
[153,] "Macrophomina_phaseolina"                 NA                              
[154,] "Magnaporthe_grisea"                      "Magnaporthe_grisea"            
[155,] "Magnaporthe_oryzae"                      "Magnaporthe_grisea"            
[156,] "Malassezia_globosa"                      "Malassezia_pachydermatis"      
[157,] "Marssonina_brunnea_f._sp._multigermtubi" NA                              
[158,] "Melampsora_larici-populina"              "Melampsora_larici-populina"    
[159,] "Meleagris_gallopavo"                     "Meleagris_gallopavo"           
[160,] "Metarhizium_acridum"                     "Metarhizium_anisopliae"        
[161,] "Methanocaldococcus_jannaschii"           NA                              
[162,] "Methanosarcina_acetivorans"              NA                              
[163,] "Meyerozyma_guilliermondii"               NA                              
[164,] "Micromonas_commoda"                      "Micromonas_pusilla"            
[165,] "Microsporum_canis"                       NA                              
[166,] "Mixia_osmundae"                          NA                              
[167,] "Moniliophthora_perniciosa"               NA                              
[168,] "Monodelphis_domestica"                   "Monodelphis_domestica"         
[169,] "Monosiga_brevicollis"                    NA                              
[170,] "Mucor_circinelloides"                    "Mucor_mucedo"                  
[171,] "Mus_musculus"                            "Mus_musculus"                  
[172,] "Mustela_putorius"                        "Mustela_putorius"              
[173,] "Mycobacterium_tuberculosis"              NA                              
[174,] "Mycosphaerella_fijiensis"                NA                              
[175,] "Mycosphaerella_graminicola"              NA                              
[176,] "Myotis_lucifugus"                        "Myotis_lucifugus"              
[177,] "Naegleria_gruberi"                       "Naegleria_gruberi"             
[178,] "Nasonia_vitripennis"                     NA                              
[179,] "Nectria_haematococca"                    "Nectria_lugdunensis"           
[180,] "Nematocida_parisii"                      NA                              
[181,] "Nematostella_vectensis"                  "'Nematostella_sp._JVK-2006'"   
[182,] "Neosartorya_fischeri"                    NA                              
[183,] "Neospora_caninum"                        NA                              
[184,] "Neurospora_crassa"                       NA                              
[185,] "Neurospora_discreta"                     NA                              
[186,] "Neurospora_tetrasperma"                  NA                              
[187,] "Nomascus_leucogenys"                     "Nomascus_leucogenys"           
[188,] "Nosema_ceranae"                          NA                              
[189,] "Oikopleura_dioica"                       NA                              
[190,] "Oreochromis_niloticus"                   "Oreochromis_andersonii"        
[191,] "Ornithorhynchus_anatinus"                "Ornithorhynchus_anatinus"      
[192,] "Oryctolagus_cuniculus"                   "Oryctolagus_cuniculus"         
[193,] "Oryza_sativa_subsp._japonica"            "Oryzaephilus_surinamensis"     
[194,] "Oryzias_latipes"                         "Oryzias_latipes"               
[195,] "Ostreococcus_tauri"                      "Ostreococcus_tauri"            
[196,] "Otolemur_garnettii"                      "Otolemur_garnettii"            
[197,] "Pan_troglodytes"                         "Pan_troglodytes"               
[198,] "Paracoccidioides_brasiliensis"           "Paracoccidioides_brasiliensis" 
[199,] "Paramecium_tetraurelia"                  "Paramecium_tetraurelia"        
[200,] "Pediculus_humanus"                       "Pediculus_humanus"             
[201,] "Penicillium_chrysogenum"                 NA                              
[202,] "Penicillium_digitatum"                   NA                              
[203,] "Penicillium_marneffei"                   NA                              
[204,] "Perkinsus_marinus"                       "Perkinsus_marinus"             
[205,] "Phaeodactylum_tricornutum"               "Phaeodactylum_tricornutum"     
[206,] "Phaeosphaeria_nodorum"                   "Phaeosphaeria_nodorum"         
[207,] "Phanerochaete_carnosa"                   "Phanerochaete_chrysosporium"   
[208,] "Phanerochaete_chrysosporium"             "Phanerochaete_chrysosporium"   
[209,] "Phycomyces_blakesleeanus"                NA                              
[210,] "Physcomitrella_patens"                   "Physcomitrella_patens"         
[211,] "Phytophthora_infestans"                  "Phytophthora_infestans"        
[212,] "Phytophthora_ramorum"                    NA                              
[213,] "Phytophthora_sojae"                      NA                              
[214,] "Pichia_pastoris"                         NA                              
[215,] "Pichia_sorbitophila"                     NA                              
[216,] "Piriformospora_indica"                   NA                              
[217,] "Plasmodium_berghei"                      "Plasmodium_berghei"            
[218,] "Plasmodium_chabaudi"                     "Plasmodium_chabaudi"           
[219,] "Plasmodium_falciparum"                   "Plasmodium_falciparum"         
[220,] "Plasmodium_knowlesi"                     "Plasmodium_knowlesi"           
[221,] "Plasmodium_vivax"                        "Plasmodium_vivax"              
[222,] "Plasmodium_yoelii"                       "Plasmodium_yoelii"             
[223,] "Pleurotus_ostreatus"                     "Pleurotus_ostreatus"           
[224,] "Pneumocystis_jiroveci"                   "Pneumocystis_carinii"          
[225,] "Podospora_anserina"                      NA                              
[226,] "Polysphondylium_pallidum"                NA                              
[227,] "Pongo_abelii"                            "Pongo_abelii"                  
[228,] "Populus_trichocarpa"                     "Populus_nigra"                 
[229,] "Postia_placenta"                         NA                              
[230,] "Pristionchus_pacificus"                  NA                              
[231,] "Pseudomonas_aeruginosa"                  NA                              
[232,] "Pteropus_alecto"                         "Pteropus_alecto"               
[233,] "Puccinia_graminis_f._sp._tritici"        NA                              
[234,] "Pyrenophora_tritici-repentis"            "Pyrenophora_tritici-repentis"  
[235,] "Pyrobaculum_aerophilum"                  NA                              
[236,] "Pyrococcus_kodakaraensis"                NA                              
[237,] "Pythium_ultimum"                         NA                              
[238,] "Rattus_norvegicus"                       "Rattus_norvegicus"             
[239,] "Rhizopus_delemar"                        NA                              
[240,] "Rhizopus_oryzae"                         NA                              
[241,] "Rhodopirellula_baltica"                  NA                              
[242,] "Rhodotorula_glutinis"                    NA                              
[243,] "Ricinus_communis"                        "Ricinus_communis"              
[244,] "Saccharomyces_bayanus"                   "Saccharomyces_bayanus"         
[245,] "Saccharomyces_castellii"                 NA                              
[246,] "Saccharomyces_cerevisiae"                "Saccharomyces_cerevisiae"      
[247,] "Saccharomyces_kluyveri"                  NA                              
[248,] "Saccharomyces_kudriavzevii"              NA                              
[249,] "Saccharomyces_mikatae"                   NA                              
[250,] "Saccharomyces_paradoxus"                 NA                              
[251,] "Salpingoeca_rosetta"                     NA                              
[252,] "Sarcophilus_harrisii"                    "Sarcophilus_harrisii"          
[253,] "Scheffersomyces_stipitis"                NA                              
[254,] "Schistosoma_mansoni"                     "Schistosoma_mekongi"           
[255,] "Schizophyllum_commune"                   "Schizophyllum_radiatum"        
[256,] "Schizosaccharomyces_cryophilus"          NA                              
[257,] "Schizosaccharomyces_japonicus"           NA                              
[258,] "Schizosaccharomyces_octosporus"          NA                              
[259,] "Schizosaccharomyces_pombe"               "Schizosaccharomyces_pombe"     
[260,] "Sclerotinia_sclerotiorum"                NA                              
[261,] "Selaginella_moellendorffii"              "Selaginella_moellendorffii"    
[262,] "Serpula_lacrymans"                       "Serpula_lacrymans"             
[263,] "Setaria_italica"                         "Setaria_viridis"               
[264,] "Solanum_lycopersicum"                    "Solanum_aviculare"             
[265,] "Solanum_tuberosum"                       "Solanum_tuberosum"             
[266,] "Solenopsis_invicta"                      "Solenopsis_invicta"            
[267,] "Sordaria_macrospora"                     "Sordaria_fimicola"             
[268,] "Sorghum_bicolor"                         "Sorghum_propinquum"            
[269,] "Spathaspora_passalidarum"                NA                              
[270,] "Spermophilus_tridecemlineatus"           "Spermophilus_erythrogenys"     
[271,] "Spizellomyces_punctatus"                 "Spizellomyces_acuminatus"      
[272,] "Sporisorium_reilianum"                   "Sporisorium_reilianum"         
[273,] "Sporobolomyces_roseus"                   NA                              
[274,] "Sporotrichum_thermophile"                NA                              
[275,] "Streptomyces_coelicolor"                 NA                              
[276,] "Strongylocentrotus_purpuratus"           "Strongylocentrotus_pallidus"   
[277,] "Sulfolobus_solfataricus"                 NA                              
[278,] "Sus_scrofa"                              "Sus_scrofa"                    
[279,] "Synechocystis_sp."                       NA                              
[280,] "Taeniopygia_guttata"                     "Taeniopygia_guttata"           
[281,] "Takifugu_rubripes"                       "Takifugu_rubripes"             
[282,] "Talaromyces_stipitatus"                  "Talaromyces_marneffei"         
[283,] "Tetrahymena_thermophila"                 "Tetrahymena_thermophila"       
[284,] "Tetraodon_nigroviridis"                  "Tetraodon_mbu"                 
[285,] "Tetrapisispora_blattae"                  NA                              
[286,] "Thalassiosira_pseudonana"                "Thalassiosira_pseudonana"      
[287,] "Theileria_annulata"                      "Theileria_parva"               
[288,] "Theileria_parva"                         "Theileria_parva"               
[289,] "Thermodesulfovibrio_yellowstonii"        NA                              
[290,] "Thermotoga_maritima"                     NA                              
[291,] "Thielavia_heterothallica"                NA                              
[292,] "Thielavia_terrestris"                    NA                              
[293,] "Torulaspora_delbrueckii"                 NA                              
[294,] "Toxoplasma_gondii"                       "Toxoplasma_gondii"             
[295,] "Trachipleistophora_hominis"              NA                              
[296,] "Tremella_mesenterica"                    "Tremella_mesenterica"          
[297,] "Tribolium_castaneum"                     "Tribolium_echinatum"           
[298,] "Trichinella_spiralis"                    NA                              
[299,] "Trichoderma_atroviride"                  NA                              
[300,] "Trichoderma_reesei"                      NA                              
[301,] "Trichomonas_vaginalis"                   "Trichomonas_vaginalis"         
[302,] "Trichophyton_equinum"                    NA                              
[303,] "Trichophyton_rubrum"                     "Trichophyton_rubrum"           
[304,] "Trichophyton_tonsurans"                  NA                              
[305,] "Trichoplax_adhaerens"                    NA                              
[306,] "Trichosporon_asahii"                     NA                              
[307,] "Trypanosoma_brucei_brucei"               NA                              
[308,] "Trypanosoma_cruzi"                       NA                              
[309,] "Tuber_melanosporum"                      "Tuberculobruchus_natalensis"   
[310,] "Tupaia_chinensis"                        "Tupaia_splendidula"            
[311,] "Uncinocarpus_reesii"                     "Uncinocarpus_reesii"           
[312,] "Ustilago_maydis"                         "Ustilago_maydis"               
[313,] "Vanderwaltozyma_polyspora"               NA                              
[314,] "Vavraia_culicis"                         NA                              
[315,] "Verticillium_alboatrum"                  NA                              
[316,] "Verticillium_dahliae"                    NA                              
[317,] "Vitis_vinifera"                          "Vitis_vinifera"                
[318,] "Vittaforma_corneae"                      NA                              
[319,] "Volvox_carteri"                          "Volvox_carteri"                
[320,] "Wallemia_sebi"                           NA                              
[321,] "Wickerhamomyces_ciferrii"                NA                              
[322,] "Wuchereria_bancrofti"                    NA                              
[323,] "Xenopus_tropicalis"                      "Xenopus_amieti"                
[324,] "Xiphophorus_maculatus"                   "Xiphophorus_maculatus"         
[325,] "Yarrowia_lipolytica"                     "Yarrowia_lipolytica"           
[326,] "Zygosaccharomyces_rouxii"                NA 

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[Alexander Ulrich]

Hi Joseph,

Thank you so much for your help and effort! 

I think you are right, since ~ 1/3 can not be included I will then most likely stick with the standard tree without branch lengths and argue with the reviewers.