Converting repeated emails into FAQs: Today's = How to Get Figures/Details from 2009 GEBA paper

OK I am now officially completely driven insane by email.  As part of my attempt to reduce email communication with people I am going to start posting some of the emails I get often into FAQs.

Today's email relates to the 2009 paper on a "Phylogeny driven genomic encyclopedia of bacteria and archaea" for which I was the senior and corresponding author.  The email is asking for higher resolution figures that were published in the paper.  This person and many others have asked for a higher res. version of our "genome tree" which was Figure 1.  Here is the version from the paper


But alas, as a JPG when you zoom in you can't see the text very well.  And about 30 or so people, maybe more, have asked for a higher res. version.  Well, the simplest way to get this figure with legible fonts when zoomed in is to get the PDF of the paper and zoom in on it.  But that may not be for everyone - so here is a link to the PDF of the figure that I posted on postures (Blogger does not allow PDF uploads).  I also posted PDFs of the other figures.



Many people also ask for the treefile (which is basically a coded version of the phylogenetic tree for viewing and analysis).  I am directly posting the treefile below and have also submitted it to "Treebase" (which we should have done before).  Enjoy ... and in the future I will be pointing people to this page when they ask for the figure/treefile. Not sure this will have saved me anytime but am sick of writing a lot of this in emails back to people ...


#NEXUS
BEGIN trees;
TREE 'Tree1' = ((((('GEBA_Thermanaerovibrio_acidaminovorans':0.190689,'GEBA_Dethiosulfovibrio_peptidovorans':0.263143):0.276658,(((((((((((((((((((((((((((((((((((((((('Escherichia_coli_O157_H7_str_Sakai':0.0,'Escherichia_coli_str_K12_substr_MG1655':0.0):1.51E-4,'Escherichia_coli_str_K12_substr_DH10B':0.0):2.0E-5,('Escherichia_coli_ATCC_8739':1.7E-4,'Escherichia_coli_HS':1.71E-4):1.7E-4):0.0,('Escherichia_coli_536':0.001196,'Escherichia_coli_APEC_O1':0.0):0.0):0.0,(('Shigella_flexneri_2a_str_301':0.001883,'Shigella_flexneri_2a_str_2457T':0.0):1.71E-4,'Shigella_flexneri_5_str_8401':3.44E-4):5.12E-4):0.0,('Shigella_boydii_CDC_3083_94':5.13E-4,'Shigella_boydii_Sb227':8.57E-4):3.42E-4):0.0,'Escherichia_coli_SMS_3_5':0.0):0.0,'Escherichia_coli_O157_H7_EDL933':0.0):0.0,'Escherichia_coli_CFT073':0.0):0.0,'Escherichia_coli_UTI89':0.0):0.0,'Escherichia_coli_E24377A':0.0):0.0,'Shigella_dysenteriae_Sd197':0.001025):1.69E-4,'Shigella_sonnei_Ss046':0.001028):0.012167,((((((('Salmonella_enterica_subsp_enterica_serovar_Typhi_str_Ty2':0.0,'Salmonella_enterica_subsp_enterica_serovar_Typhi_str_CT18':1.7E-4):3.4E-4,'Salmonella_typhimurium_LT2':0.0):0.0,'Salmonella_enterica_subsp_enterica_serovar_Paratyphi_A_str_ATCC_9150':8.5E-4):2.0E-6,'Salmonella_enterica_subsp_enterica_serovar_Paratyphi_B_str_SPB7':1.8E-4):1.69E-4,'Salmonella_enterica_subsp_enterica_serovar_Choleraesuis_str_SC_B67':3.48E-4):0.001774,'Salmonella_enterica_subsp_arizonae_serovar_62_z4_z23_':0.001673):0.008533,'Citrobacter_koseri_ATCC_BAA_895':0.007106):0.003103):0.00437,'Klebsiella_pneumoniae_subsp_pneumoniae_MGH_78578':0.012094):0.004392,'Enterobacter_sakazakii_ATCC_BAA_894':0.019781):0.007021,'Enterobacter_sp_638':0.019532):0.027075,('Erwinia_tasmaniensis':0.033979,'Serratia_proteamaculans_568':0.033607):0.013319):0.008604,'Erwinia_carotovora_subsp_atroseptica_SCRI1043':0.03122):0.012206,(((((('Yersinia_pestis_KIM':0.0,'Yersinia_pseudotuberculosis_IP_31758':0.0):0.0,'Yersinia_pestis_CO92':0.0):0.0,'Yersinia_pseudotuberculosis_IP_32953':0.0):0.0,(((('Yersinia_pseudotuberculosis_PB1_':0.0,'Yersinia_pestis_Pestoides_F':0.0):0.0,('Yersinia_pseudotuberculosis_YPIII':0.0,'Yersinia_pestis_Nepal516':0.0):0.0):0.0,'Yersinia_pestis_Antiqua':1.72E-4):0.0,'Yersinia_pestis_biovar_Microtus_str_91001':0.0):0.0):0.0,'Yersinia_pestis_Angola':3.44E-4):0.00575,'Yersinia_enterocolitica_subsp_enterocolitica_8081':0.009468):0.030284):0.008222,(((('Candidatus_Blochmannia_pennsylvanicus_str_BPEN':0.111832,'Candidatus_Blochmannia_floridanus':0.199319):0.14508,((('Buchnera_aphidicola_str_APS_Acyrthosiphon_pisum_':0.081646,'Buchnera_aphidicola_str_Sg_Schizaphis_graminum_':0.078489):0.090786,'Buchnera_aphidicola_str_Bp_Baizongia_pistaciae_':0.232468):0.043831,('Wigglesworthia_glossinidia_endosymbiont_of_Glossina_brevipalpis':0.30099,'Buchnera_aphidicola_str_Cc_Cinara_cedri_':0.303142):0.063766):0.064196):0.054991,'Baumannia_cicadellinicola_str_Hc_Homalodisca_coagulata_':0.166451):0.081445,'Sodalis_glossinidius_str_morsitans_':0.026696):0.024889):0.01239,'Photorhabdus_luminescens_subsp_laumondii_TTO1':0.048195):0.050763,(((('Haemophilus_somnus_129PT':9.73E-4,'Haemophilus_somnus_2336':7.28E-4):0.038446,'Pasteurella_multocida_subsp_multocida_str_Pm70':0.033371):0.011204,(('Mannheimia_succiniciproducens_MBEL55E':0.02899,'Actinobacillus_succinogenes_130Z':0.035825):0.013874,((('Haemophilus_influenzae_Rd_KW20':0.002043,'Haemophilus_influenzae_PittGG':0.00105):5.49E-4,'Haemophilus_influenzae_86_028NP':5.15E-4):2.24E-4,'Haemophilus_influenzae_PittEE':0.001026):0.040304):0.008478):0.011217,((('Actinobacillus_pleuropneumoniae_L20':0.00137,'Actinobacillus_pleuropneumoniae_serovar_7_str_AP76':3.39E-4):1.74E-4,'Actinobacillus_pleuropneumoniae_serovar_3_str_JL03':0.003062):0.011765,'Haemophilus_ducreyi_35000HP':0.024577):0.038512):0.080775):0.047571,((((('Vibrio_cholerae_O1_biovar_eltor_str_N16961':3.64E-4,'Vibrio_cholerae_O395':8.38E-4):0.041305,('Vibrio_vulnificus_CMCP6':5.27E-4,'Vibrio_vulnificus_YJ016':1.72E-4):0.020829):0.011445,('Vibrio_parahaemolyticus_RIMD_2210633':0.00625,'Vibrio_harveyi_ATCC_BAA_1116':0.010839):0.011481):0.027253,'Vibrio_fischeri_ES114':0.05376):0.027779,'Photobacterium_profundum_SS9':0.072105):0.054993):0.023142,('Aeromonas_hydrophila_subsp_hydrophila_ATCC_7966':0.006284,'Aeromonas_salmonicida_subsp_salmonicida_A449':0.0108):0.109795):0.020707,(((((('Shewanella_halifaxensis_HAW_EB4':0.008905,'Shewanella_pealeana_ATCC_700345':0.003805):0.025082,('Shewanella_sediminis_HAW_EB3':0.019306,'Shewanella_woodyi_ATCC_51908':0.012326):0.017175):0.016987,'Shewanella_loihica_PV_4':0.021173):0.024752,(((((('Shewanella_sp_ANA_3':0.002092,'Shewanella_sp_MR_4':9.8E-4):7.54E-4,'Shewanella_sp_MR_7':3.48E-4):0.003036,'Shewanella_oneidensis_MR_1':0.002265):0.010027,('Shewanella_sp_W3_18_1':3.26E-4,'Shewanella_putrefaciens_CN_32':1.85E-4):0.001996):0.006463,(('Shewanella_baltica_OS155':0.001236,'Shewanella_baltica_OS195':0.0):5.23E-4,'Shewanella_baltica_OS185':6.84E-4):0.009966):0.015626,('Shewanella_denitr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Tropheryma_whipplei_str_Twist':6.79E-4):0.478476):0.120846,'GEBA_Acidimicrobium_ferrooxidans':0.43829):0.090081,((('GEBA_Cryptobacterium_curtum':0.142154,'GEBA_Eggerthella_lenta':0.088587):0.047811,'GEBA_Slackia_heliotrinireducens':0.117231):0.104268,'GEBA_Atopobium_parvulum':0.269623):0.198082):0.036936,('GEBA_Conexibacter_woesei':0.383152,'Rubrobacter_xylanophilus_DSM_9941':0.357989):0.109409):0.087352,((((((((('Synechococcus_sp_WH_7803':0.023543,'Synechococcus_sp_CC9311':0.044194):0.014221,(('Synechococcus_sp_CC9605':0.022222,'Synechococcus_sp_WH_8102':0.025798):0.006423,'Synechococcus_sp_CC9902':0.032326):0.022152):0.016325,((('Prochlorococcus_marinus_subsp_marinus_str_CCMP1375':0.058394,'Prochlorococcus_marinus_str_MIT_9211':0.053438):0.019947,(('Prochlorococcus_marinus_str_NATL2A':0.00276,'Prochlorococcus_marinus_str_NATL1A':0.002109):0.070906,(('Prochlorococcus_marinus_str_MIT_9515':0.013908,'Prochlorococcus_marinus_subsp_pastoris_str_CCMP1986':0.016702):0.023743,((('Prochlorococcus_marinus_str_AS9601':0.005031,'Prochlorococcus_marinus_str_MIT_9301':0.005416):0.003975,'Prochlorococcus_marinus_str_MIT_9215':0.011185):0.004908,'Prochlorococcus_marinus_str_MIT_9312':0.010415):0.020455):0.117983):0.022565):0.040798,('Prochlorococcus_marinus_str_MIT_9313':0.00429,'Prochlorococcus_marinus_str_MIT_9303':0.003453):0.043557):0.012995):0.046129,'Synechococcus_sp_RCC307':0.067465):0.195828,('Synechococcus_elongatus_PCC_7942':3.21E-4,'Synechococcus_elongatus_PCC_6301':0.00142):0.098101):0.061386,((((('Nostoc_sp_PCC_7120':0.004827,'Anabaena_variabilis_ATCC_29413':0.003501):0.036361,'Nostoc_punctiforme_PCC_73102':0.042386):0.086848,'Trichodesmium_erythraeum_IMS101':0.151445):0.024405,((('Cyanothece_sp_ATCC_51142':0.088208,'Microcystis_aeruginosa_NIES_843':0.108904):0.018975,'Synechocystis_sp_PCC_6803':0.111161):0.027275,'Synechococcus_sp_PCC_7002':0.127272):0.053965):0.023778,('Acaryochloris_marina_MBIC11017':0.127345,'Thermosynechococcus_elongatus_BP_1':0.138774):0.035212):0.017944):0.063385,('Synechococcus_sp_JA_3_3Ab':0.023735,'Synechococcus_sp_JA_2_3B_a_2_13_':0.025648):0.172906):0.056598,'Gloeobacter_violaceus_PCC_7421':0.211642):0.301851,((((('Roseiflexus_castenholzii_DSM_13941':0.02822,'Roseiflexus_sp_RS_1':0.017828):0.118476,'Chloroflexus_aurantiacus_J_10_fl':0.154341):0.066504,'Herpetosiphon_aurantiacus_ATCC_23779':0.219302):0.124086,('GEBA_Sphaerobacter_thermophilus':0.242004,'GEBA_Thermobaculum_terrenum':0.272557):0.055029):0.055648,(('Dehalococcoides_sp_CBDB1':5.54E-4,'Dehalococcoides_sp_BAV1':8.51E-4):0.017643,'Dehalococcoides_ethenogenes_195':0.014048):0.50406):0.083393):0.032459):0.039409):0.035188):0.022061):0.039665):0.054226,((('Thermosipho_melanesiensis_BI429':0.127803,'Fervidobacterium_nodosum_Rt17_B1':0.188887):0.074834,((('Thermotoga_maritima_MSB8':0.007577,'Thermotoga_sp_RQ2':5.3E-4):0.005057,'Thermotoga_petrophila_RKU_1':0.006656):0.159923,'Thermotoga_lettingae_TMO':0.230211):0.037393):0.080613,'Petrotoga_mobilis_SJ95':0.362128):0.246177):0.287154,(('Thermus_thermophilus_HB8':0.001498,'Thermus_thermophilus_HB27':0.001224):0.144321,('GEBA_Meiothermus_ruber':0.114423,'GEBA_Meiothermus_silvanus':0.077947):0.086289):0.12529):0.1212895,('Deinococcus_geothermalis_DSM_11300':0.043888,'Deinococcus_radiodurans_R1':0.07314):0.1212895);
END;







4 comments:

  1. + you've already got the aligned sequence data and tree on TreeBASE here: http://www.treebase.org/treebase-web/search/study/summary.html?id=10965

    Thanks for doing that, you're setting a good example IMO.

    I wish all data matrices and trees were put online in their 'raw', usable form (rather than as PDFs). TreeBASE deposition is rather the exception than the rule atm :(

    ReplyDelete
    Replies
    1. woops, didnt quite read to the end of your post. So you've only just deposited it in TreeBASE? well... better late than never I guess! :)

      Delete
  2. Well, what we did in 2009 was post the raw tree file and alignments and such on my lab web site. But that is not the most visible place. So TreeBASE and other places are clearly much better. For recent papers we have also been trying to deposit everything in Dryad ...

    ReplyDelete
  3. Ross --- actually --- just discovered that the entry you link to was uploaded by someone other than me --- most likely was one of the other authors --- gonna have to dig around but I don't remember anyone telling me they did this --- but whomever did it also uploaded the alignment and taxon information ---

    ReplyDelete