More trees for your viewing dismay

A few days ago I posted a NJ 1000 bootstrapped cyanobacteria tree at the genera level. Here are a couple of other ways to look at the same data set.

Image

This is an AML tree. You can see some things are in different places.
The big difference I noticed was the placement of the candidatus genera.

Both the NJ and AML tree are different from the NCBI taxonomic structure.

I’ll post the PhyML tree later today.

I am going to remove the short sequences from the cyano tree, run a new alignment, and then compare the trees again.

The newick file for this tree is here:

((((((Limnococcus:0.0543055396,Johannesbaptistia:0.0827145140)70:0.0344450208,Chondrocystis:0.0729476463)53:0.0279920338,(((Solentia:0.0565478859,Hyella:0.0558046996)59:0.0149440458,(Myxosarcina:0.0143627100,((Dermocarpa:0.0090838586,Stanieria:0.0298887512)100:0.0319212685,((Xenococcus:0.0306654901,Pleurocapsa:0.0529666329)97:0.0263862958,Dermocarpella:0.0307601085)84:0.0165593063)59:0.0083008678)100:0.0624117043)43:0.0393172329,(((((((((((Trichocoleus:0.0845592526,Chroogloeocystis:0.0594235144)52:0.0263768491,(Chroococcus:0.0880145666,Chroococcidiopsis:0.1275603493)56:0.0223390003)15:0.0163417632,(Microchaete:3.2941937902,(((((Crinalium:0.0008802610,Starria:0.0725556714)99:0.0769356244,Chamaesiphon:0.1220433027)42:0.0266538083,(((((((Cylindrospermum:0.0430895087,((((((Coleodesmium:0.0019855000,Rexia:0.0185910119)90:0.0149691424,Hassallia:0.0179228155)77:0.0124770313,(Pseudoscytonema:0.0305139345,Uncultured_Richelia:0.0649750928)59:0.0267823784)63:0.0169522963,Spirirestis:0.0399104672)46:0.0345921707,(Mojavia:0.0502289833,Tolypothrix:0.0047592151)72:0.0131213010)17:0.0077281451,((((Calothrix:0.0085082496,Anabaena:0.0897209192)55:0.0151979445,Camptylonemopsis:0.0178761361)58:0.0173368772,(Trichormus:0.0409631812,Anabaenopsis:0.0308688459)98:0.0507930721)25:0.0087945825,(Fortiea:0.0599328005,Nostoc:0.0318855257)18:0.0076194233)8:0.0135365193)2:0.0092326146)4:0.0038240170,(((Raphidiopsis:0.0084712314,Cylindrospermopsis:0.0067275585)100:0.0350623875,Sphaerospermopsis:0.0266622460)98:0.0342990146,Wollea:0.0392845032)99:0.0480554525)0:0.0082196991,((((Cyanospira:0.0272434458,Nodularia:0.0303054134)74:0.0166932171,Umezakia:0.0358745909)66:0.0096985007,((Dolichospermum:0.0013565773,Aphanizomenon:0.0063531148)100:0.0390046417,Cuspidothrix:0.0490716892)97:0.0307378581)16:0.0039297611,Gloeotrichia:0.1261188474)12:0.0121215958)15:0.0179228257,(Stigonema:0.0438563149,(Petalonema:0.0339177052,Capsosira:0.0581682710)44:0.0240729296)16:0.0197428491)32:0.0171179575,(((((Westiellopsis:0.0152923821,Hapalosiphon:0.0290265101)71:0.0204530495,Nostochopsis:0.0192930816)100:0.0375972724,(Mastigocladus:0.0011028859,Fischerella:0.0026556062)100:0.0888819220)78:0.0265307267,Chlorogloeopsis:0.1031979664)63:0.0138862847,Rivularia:0.1015247325)32:0.0126707007)16:0.0086900666,Scytonematopsis:0.1270558400)37:0.0082529310,((Brasilonema:0.0375396638,((Iphinoe:0.0114128798,Symphyonemopsis:0.0159845680)100:0.0319429392,Scytonema:0.1118834077)35:0.0082325641)50:0.0200321933,(Mastigocladopsis:0.0363274273,Symphyonema:0.0514882467)72:0.0255197169)72:0.0216286012)68:0.0382440977)6:0.0223698398,(Wilmottia:0.0280695032,Hormoscilla:0.0194230275)100:0.0806008070)1:0.0012637447,(Loriellopsis:0.0916794075,Plectonema:0.1246701722)29:0.0364987647)1:0.0065504130)0:0.0000213631)1:0.0231823214,Pseudanabaena:0.1656468029)0:0.0048665047,((Methanocaldococcus:4.5620715748,Symploca:0.0499612094)1:0.0000242825,(Moorea:0.0424026717,Schizothrix:0.0603348702)93:0.0454078928)1:0.0337228245)0:0.0086556421,((Oscillatoria:0.0180910320,Phormidium:0.0038345668)100:0.1083669419,(Planktothricoides:0.1474494446,((Desertifilum:0.1231389559,Pseudoscillatoria:0.1172493477)64:0.0608279908,(((Tychonema:0.0247008096,Microcoleus:0.0255393621)100:0.0621785623,(((Symplocastrum:0.0017341035,Blennothrix:0.0127629204)71:0.0118772978,Hydrocoleum:0.0464332764)44:0.0101616270,Trichodesmium:0.0262792138)100:0.0738871439)44:0.0112265496,(((Arthrospira:0.0036035480,Spirulina:0.0034321365)100:0.0496378848,Lyngbya:0.0520722943)89:0.0254526616,Planktothrix:0.1574632224)17:0.0182371747)18:0.0106061863)1:0.0027617597)0:0.0064997552)2:0.0203181605)0:0.0149033793,((((Planktolyngbya:0.0649382523,Limnothrix:0.1970967400)30:0.0523259811,((Tapinothrix:0.1083835743,Plectolyngbya:0.0848674559)79:0.0494241348,Romeria:0.1394751273)54:0.0449033338)10:0.0332090681,Arthronema:0.0882816659)8:0.0416833591,((((Thermosynechococcus:0.0177456642,Synechococcus:0.0048970458)100:0.0936297297,Aphanocapsa:0.0431221365)65:0.0265767257,Acaryochloris:0.1130397694)30:0.0215642832,(((((Halomicronema:0.0859311198,(Nodosilinea:0.0527282792,Haloleptolyngbya:0.0692337431)99:0.0491872765)24:0.0181959139,(Leptolyngbya:0.1061522162,Pseudophormidium:0.0861900283)42:0.0285976662)21:0.0218354835,Prochlorothrix:0.1039802682)19:0.0075813211,(Jaaginema:0.1439699514,(Merismopedia:0.0194576660,((Prochlorococcus:0.0667450851,Cyanodictyon:0.0030830827)52:0.0063483954,Cyanobium:0.0096935315)59:0.0087606677)92:0.1194728238)17:0.0366526652)11:0.0203338112,(Gloeobacter:0.1642330110,Chlorogloea:0.1038778876)25:0.0605400448)6:0.0359408989)1:0.0099348650)0:0.0244375123)2:0.0317513322,Prochloron:0.1034279892)1:0.0075801850,((Chroococcopsis:0.0949580129,Cyanobacterium:0.0787609893)96:0.1207597758,(((Halospirulina:0.0559544587,Aulosira:0.1579393772)85:0.0616160327,Geitlerinema:0.1273880648)15:0.0169191192,((Dactylococcopsis:0.0459940135,Cyanothece:0.0350513305)100:0.0950093180,(Rubidibacter:0.0958104807,Halothece:0.1030371781)81:0.0446507128)49:0.0236324398)33:0.0219272790)5:0.0116565596)1:0.0094555589,(Rhabdoderma:0.1119214060,(((Radiocystis:0.0931314877,Gloeothece:0.0579325054)58:0.0190687488,Microcystis:0.1026691837)53:0.0179869029,((Woronichinia:0.0393573655,Snowella:0.0676299563)98:0.0367508722,Synechocystis:0.0479859932)91:0.0365259331)78:0.0205312028)5:0.0136663395)0:0.0071853366,Komvophoron:0.1378140913)0:0.0049130416)0:0.0105862343)0:0.0239406424,Aphanothece:0.0553651193)1:0.0586166557,(Gloeocapsa:0.0217367744,Crocosphaera:0.0161067250)90:0.0000065241)27:0.1966092526,Cyanosarcina:0.1393880769,Gloeocapsopsis:2.5790516588);

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7 Responses to More trees for your viewing dismay

  1. Dr Pawan K Dadheech says:

    I found this clockwise tree very informative but it can be viewed only on screen but not clearly printed because of very small fonts. It seems that newick file of this tree is incomplete. Please upload a complete functional newick file. It will be better to mentioned how much nt used for construction of the tree.

    • clockworkscience says:

      The whole tree is there but WordPress is cutting off the last part of it for some reason. I’ll see if I can set up a link to the tree file.

  2. clockworkscience says:

    If you double click on the bottom of the tree and the copy it you will end up with the whole tree.

  3. Dr Pawan K Dadheech says:

    Yes, it is possible to copy the tree but when it is printed in A4 size paper the genera names are visible due to very small font size and even lines of lineages are also not clear. It would be better to provide a link to download a functional newick file.

    • Dr Pawan K Dadheech says:

      Thanks for sending the link and it works well. Looking the tree, It is surprising to see phylogenetic distinctness between Cyanospira and Anabaenopsis as they share more or less 98% similarity in 16S rRNA gene sequence.

      • A couple things are going on here. The tree you are currently looking at is an AML tree rooted with chloroflexi. I am building three more trees so compare. Also the cyano data set has a large number of short seqeuences which will through the alignment and tree off.

        I’ll have a full workup of the various cyano trees in a few days.

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