Possible bugs in bootstrap trees RAxML.7.2.8?
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Jess
Nov 11, 2011, 11:12:06 AM11/11/11
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Hello,
I've just been trying to create bootstrap consensus trees in RAxML.
7.2.8 and have come across some problems.
Firstly, when trying to create the three consensus trees, (in the -J
option - MR, MRE or STRICT), if I go to open them in figtree (or
treeedit) I get the error message: "Import Error: Error reading tree
file: Missing closing ')' in tree"
However, clearly this isn't the case, (there are the same number of
'(' and ')' brackets - and adding an extra ')' gives you the same
error message). Is this something to do with the way the consensus
tree allows polytomies at the root or something? The best trees all
open fine in figtree. It would be really great to be able to view
these consensus trees in figtree - but I can't work out how to correct
the consensus tree as it is produced from RAxML into something that
figtree will import. (I have pasted the MR tree below)
The second problem I have is that when drawing the bootstraps onto the
best tree (-f b) to create the bipartitions tree file, v7.2.8 produces
a bipartitions tree that is different to the best tree. In the
particular dataset I was using, it created a massive root branchlength
of 0.45. Calling exactly the same command on the old v7.0.4 version of
RAxML produced the correct best-tree with bootstraps.
I am happy to send you any of the files if that would help, otherwise
I have pasted the tree files below.
I would be very grateful if anyone is able to help with this. Many
thanks.
MR tree:
(D_torquatus_E_Kolyma2(79_layer12_M4D_6,49_layer12_M3_1,150_UK_Yngr_dryas,
(D_hudsonius_b,
((E023,144_layer16_C7_19,E015,E012,E050,E051,E029,E049,E018,E019,
(E052,E024,(E027,E020):1.0[83]):1.0[64]):1.0[75],(E026,(E036,E014):
1.0[68]):1.0[52]):1.0[62],
(((129_layer12_M4_6,134_Layer14_K6_9,146_layer16_M7_16,135_layer14_D7_16,133_layer14_K6_9,
(132_layer14_K7_9,145_layer16_M7_16):1.0[68]):1.0[85],
(130_12_M4_6_Haplo,136_layer14_D7_16):1.0[58]):1.0[57],(E047,
(131_layer12_M4_6,48_layer12_M3_9,47_layer12_M3_9):1.0[65]):1.0[64]):
1.0[78],(56_12_M4_5_Haplo,
46_layer12_M3_9,80_layer12_M4D_6,54_12_M4_5_Haplo,
86_layer12_M4D_6,73_layer12_M4D_6,62_layer12_M4_5,57_12_M4_5_Haplo,
66_layer12_M4_5,(65_layer12_M4_5,71_layer12_M4D_6):1.0[52]):1.0[76]):
1.0[66],(126_layer12_M3_2,(51_layer12_M3_1,128_12_M3_2_Haplo):1.0[56]):
1.0[65],(D_torquatus_Yamal,(D_torquatus_Pechora,D_torquatus_Kanin):
1.0[67]):1.0[61],(D_torquatus_Taymyr,D_torquatus_Taymyr2):1.0[99],
(153_UK_Yngr_dryas,149_UK_dryas_Haplo):1.0[73],
(D_torquatus_W_Kolyma,D_torquatus_Olenski):1.0[73]):1.0[61],
(D_torquatus_E_Kolyma,D_torquatus_E_Kolyma3):1.0[100]);
bipartition-bootstrap analysis called: ./raxmlHPC -m GTRGAMMA -f b -t
RAxML_bestTree.dicro.best.tre -z RAxML_bootstrap.dicro.boots -n
dicro.bip.2 -o D_hudsonius_b
besttree: ((((((48_layer12_M3_9:0.00000363619534575013,
(47_layer12_M3_9:0.00129942266970888877,131_layer12_M4_6:0.00131404211215039321):
0.00000363619534575013):
0.00132730118271114994,E047:0.00130513155135699973):
0.00134846575657471333,((((133_layer14_K6_9:0.00134145769075794011,
(135_layer14_D7_16:0.00271945986349485073,
(129_layer12_M4_6:0.00546163750744719286,146_layer16_M7_16:0.00000363619534575013):
0.00133568851414785777):0.00000363619534575013):
0.00000363619534575013,134_Layer14_K6_9:0.00000363619534575013):
0.00000363619534575013,
(145_layer16_M7_16:0.00132774593050852567,132_layer14_K7_9:0.00000363619534575013):
0.00133713032142029464):0.00278647994986401396,
(136_layer14_D7_16:0.00000363619534575013,130_12_M4_6_Haplo:
0.00131994653001272968):0.00141651841126976832):
0.00125910185854779654):0.00403005260407361416,
((62_layer12_M4_5:0.00126937068342301146,
((86_layer12_M4D_6:0.00128584289693581526,
(73_layer12_M4D_6:0.00128363904623272625,57_12_M4_5_Haplo:
0.00000363619534575013):0.00000363619534575013):0.00000363619534575013,
(((66_layer12_M4_5:0.00128838377089412386,54_12_M4_5_Haplo:
0.00128853886813459946):0.00000363619534575013,
(((65_layer12_M4_5:0.00128884461869839973,71_layer12_M4D_6:0.00000363619534575013):
0.00000363619534575013,46_layer12_M3_9:0.00000363619534575013):
0.00000363619534575013,56_12_M4_5_Haplo:0.00000363619534575013):
0.00000363619534575013):
0.00000363619534575013,80_layer12_M4D_6:0.00129274952360672085):
0.00128747536906372701):0.00130570538219615829):0.00817091584735905874,
(49_layer12_M3_1:0.00256999670460223003,(((((D_torquatus_E_Kolyma:
0.00120531358297111383,D_torquatus_E_Kolyma3:0.00000363619534575013):
0.00771015462378700587,D_torquatus_E_Kolyma2:0.00497959377899245825):
0.00395369005417124230,79_layer12_M4D_6:0.00124108783173599549):
0.00000363619534575013,(126_layer12_M3_2:0.00125541203451745163,
(51_layer12_M3_1:0.00000363619534575013,128_12_M3_2_Haplo:
0.00000363619534575013):0.00000363619534575013):
0.00124131096933333888):0.00000363619534575013,(((D_torquatus_Taymyr:
0.00000363619534575013,D_torquatus_Taymyr2:0.00000363619534575013):
0.00517034449906722277,((D_torquatus_Yamal:0.00265788371535682563,
(D_torquatus_Pechora:0.00260245233305352475,D_torquatus_Kanin:
0.00522030069062469609):0.00128598315030102996):0.00128459424545687923,
(150_UK_Yngr_dryas:0.00520455735781596464,(149_UK_dryas_Haplo:
0.00125427769367385147,153_UK_Yngr_dryas:0.00000363619534575013):
0.00000363619534575013):0.00000363619534575013):
0.00000363619534575013):0.00127745439282606044,(D_torquatus_W_Kolyma:
0.00259264052177891153,D_torquatus_Olenski:0.00122822421295203338):
0.00261310670036057598):0.00124373314667413411):
0.00000363619534575013):0.00403594532436997271):
0.00106724494576406663):0.00266572786165118845,
((E026:0.00206182631963185582,
(E036:0.00000363619534575013,E014:0.00262369135172486109):
0.00185264307150822920):0.00258387553564366377,
(((E019:0.00131795249856911140,((E049:0.00267010389584985573,
(E029:0.00000363619534575013,(E051:0.00844430881099344881,
(E050:0.00142855263970429001,
((E020:0.00144999712504058635,E027:0.00983731550324775349):
0.00539467881618129093,
(E052:0.00264611972331375844,E024:0.00000363619534575013):
0.00000363619534575013):0.00411087587953217360):
0.00278091458703202867):0.00130152933468939518):
0.00135011154385100045):
0.00131564916088999112,E018:0.00000363619534575013):
0.00000363619534575013):
0.00130834356062447198,E023:0.00000363619534575013):
0.00000363619534575013,
((144_layer16_C7_19:0.01276570132063204431,E015:0.00866622710162602734):
0.00567997135407338500,E012:0.00234361438279412837):
0.00165979415839065956):0.00761133019019519068):
0.00198464714858766602):0.02682618930035064048,D_hudsonius_b:
0.02682618930035064048);
bipartition tree:
((((((48_layer12_M3_9:0.00000363619534575013,
(47_layer12_M3_9:0.00129942266970888877,131_layer12_M4_6:0.00131404211215039321)16:0.00000363619534575013)65:0.00132730118271114994,E047:0.00130513155135699973)64:0.00134846575657471333,
((((133_layer14_K6_9:0.00134145769075794011,
(135_layer14_D7_16:0.00271945986349485073,
(129_layer12_M4_6:0.00546163750744719286,146_layer16_M7_16:0.00000363619534575013)47:0.00133568851414785777)17:0.00000363619534575013)4:0.00000363619534575013,134_Layer14_K6_9:0.00000363619534575013)12:0.00000363619534575013,
(145_layer16_M7_16:0.00132774593050852567,132_layer14_K7_9:0.00000363619534575013)68:0.00133713032142029464)85:0.00278647994986401396,
(136_layer14_D7_16:0.00000363619534575013,130_12_M4_6_Haplo:
0.00131994653001272968)58:0.00141651841126976832)57:0.00125910185854779654)78:0.00403005260407361416,
((62_layer12_M4_5:0.00126937068342301146,
((86_layer12_M4D_6:0.00128584289693581526,
(73_layer12_M4D_6:0.00128363904623272625,57_12_M4_5_Haplo:
0.00000363619534575013)19:0.00000363619534575013)26:0.00000363619534575013,
(((66_layer12_M4_5:0.00128838377089412386,54_12_M4_5_Haplo:
0.00128853886813459946)7:0.00000363619534575013,
(((65_layer12_M4_5:0.00128884461869839973,71_layer12_M4D_6:0.00000363619534575013)52:0.00000363619534575013,46_layer12_M3_9:0.00000363619534575013)4:0.00000363619534575013,56_12_M4_5_Haplo:
0.00000363619534575013)8:0.00000363619534575013)12:0.00000363619534575013,80_layer12_M4D_6:0.00129274952360672085)26:0.00128747536906372701)38:0.00130570538219615829)76:0.00817091584735905874,
(49_layer12_M3_1:0.00256999670460223003,(((((D_torquatus_E_Kolyma:
0.00120531358297111383,D_torquatus_E_Kolyma3:0.00000363619534575013)100:0.00771015462378700587,D_torquatus_E_Kolyma2:0.00497959377899245825)61:0.00395369005417124230,79_layer12_M4D_6:0.00124108783173599549)11:0.00000363619534575013,
(126_layer12_M3_2:0.00125541203451745163,
(51_layer12_M3_1:0.00000363619534575013,128_12_M3_2_Haplo:
0.00000363619534575013)56:0.00000363619534575013)65:0.00124131096933333888)5:0.00000363619534575013,
(((D_torquatus_Taymyr:
0.00000363619534575013,D_torquatus_Taymyr2:0.00000363619534575013)99:0.00517034449906722277,
((D_torquatus_Yamal:0.00265788371535682563,(D_torquatus_Pechora:
0.00260245233305352475,D_torquatus_Kanin:
0.00522030069062469609)67:0.00128598315030102996)61:0.00128459424545687923,
(150_UK_Yngr_dryas:0.00520455735781596464,(149_UK_dryas_Haplo:
0.00125427769367385147,153_UK_Yngr_dryas:
0.00000363619534575013)73:0.00000363619534575013)26:0.00000363619534575013)8:0.00000363619534575013)31:0.00127745439282606044,
(D_torquatus_W_Kolyma:0.00259264052177891153,D_torquatus_Olenski:
0.00122822421295203338)73:0.00261310670036057598)35:0.00124373314667413411)11:0.00000363619534575013)66:0.00403594532436997271)24:0.00106724494576406663)33:0.00266572786165118845,
((E026:0.00206182631963185582,
(E036:0.00000363619534575013,E014:0.00262369135172486109)68:0.00185264307150822920)52:0.00258387553564366377,
(((E019:0.00131795249856911140,((E049:0.00267010389584985573,
(E029:0.00000363619534575013,(E051:0.00844430881099344881,
(E050:0.00142855263970429001,
((E020:0.00144999712504058635,E027:0.00983731550324775349)83:0.00539467881618129093,
(E052:0.00264611972331375844,E024:0.00000363619534575013)34:0.00000363619534575013)64:0.00411087587953217360)49:0.00278091458703202867)23:0.00130152933468939518)27:0.00135011154385100045)30:0.00131564916088999112,E018:0.00000363619534575013)4:0.00000363619534575013)17:0.00130834356062447198,E023:0.00000363619534575013)12:0.00000363619534575013,
((144_layer16_C7_19:0.01276570132063204431,E015:0.00866622710162602734)48:0.00567997135407338500,E012:0.00234361438279412837)22:0.00165979415839065956)75:0.00761133019019519068)62:0.00198464714858766602):
0.45000000000000001110,D_hudsonius_b:0.45000000000000001110);
I've just been trying to create bootstrap consensus trees in RAxML.
7.2.8 and have come across some problems.
Firstly, when trying to create the three consensus trees, (in the -J
option - MR, MRE or STRICT), if I go to open them in figtree (or
treeedit) I get the error message: "Import Error: Error reading tree
file: Missing closing ')' in tree"
However, clearly this isn't the case, (there are the same number of
'(' and ')' brackets - and adding an extra ')' gives you the same
error message). Is this something to do with the way the consensus
tree allows polytomies at the root or something? The best trees all
open fine in figtree. It would be really great to be able to view
these consensus trees in figtree - but I can't work out how to correct
the consensus tree as it is produced from RAxML into something that
figtree will import. (I have pasted the MR tree below)
The second problem I have is that when drawing the bootstraps onto the
best tree (-f b) to create the bipartitions tree file, v7.2.8 produces
a bipartitions tree that is different to the best tree. In the
particular dataset I was using, it created a massive root branchlength
of 0.45. Calling exactly the same command on the old v7.0.4 version of
RAxML produced the correct best-tree with bootstraps.
I am happy to send you any of the files if that would help, otherwise
I have pasted the tree files below.
I would be very grateful if anyone is able to help with this. Many
thanks.
MR tree:
(D_torquatus_E_Kolyma2(79_layer12_M4D_6,49_layer12_M3_1,150_UK_Yngr_dryas,
(D_hudsonius_b,
((E023,144_layer16_C7_19,E015,E012,E050,E051,E029,E049,E018,E019,
(E052,E024,(E027,E020):1.0[83]):1.0[64]):1.0[75],(E026,(E036,E014):
1.0[68]):1.0[52]):1.0[62],
(((129_layer12_M4_6,134_Layer14_K6_9,146_layer16_M7_16,135_layer14_D7_16,133_layer14_K6_9,
(132_layer14_K7_9,145_layer16_M7_16):1.0[68]):1.0[85],
(130_12_M4_6_Haplo,136_layer14_D7_16):1.0[58]):1.0[57],(E047,
(131_layer12_M4_6,48_layer12_M3_9,47_layer12_M3_9):1.0[65]):1.0[64]):
1.0[78],(56_12_M4_5_Haplo,
46_layer12_M3_9,80_layer12_M4D_6,54_12_M4_5_Haplo,
86_layer12_M4D_6,73_layer12_M4D_6,62_layer12_M4_5,57_12_M4_5_Haplo,
66_layer12_M4_5,(65_layer12_M4_5,71_layer12_M4D_6):1.0[52]):1.0[76]):
1.0[66],(126_layer12_M3_2,(51_layer12_M3_1,128_12_M3_2_Haplo):1.0[56]):
1.0[65],(D_torquatus_Yamal,(D_torquatus_Pechora,D_torquatus_Kanin):
1.0[67]):1.0[61],(D_torquatus_Taymyr,D_torquatus_Taymyr2):1.0[99],
(153_UK_Yngr_dryas,149_UK_dryas_Haplo):1.0[73],
(D_torquatus_W_Kolyma,D_torquatus_Olenski):1.0[73]):1.0[61],
(D_torquatus_E_Kolyma,D_torquatus_E_Kolyma3):1.0[100]);
bipartition-bootstrap analysis called: ./raxmlHPC -m GTRGAMMA -f b -t
RAxML_bestTree.dicro.best.tre -z RAxML_bootstrap.dicro.boots -n
dicro.bip.2 -o D_hudsonius_b
besttree: ((((((48_layer12_M3_9:0.00000363619534575013,
(47_layer12_M3_9:0.00129942266970888877,131_layer12_M4_6:0.00131404211215039321):
0.00000363619534575013):
0.00132730118271114994,E047:0.00130513155135699973):
0.00134846575657471333,((((133_layer14_K6_9:0.00134145769075794011,
(135_layer14_D7_16:0.00271945986349485073,
(129_layer12_M4_6:0.00546163750744719286,146_layer16_M7_16:0.00000363619534575013):
0.00133568851414785777):0.00000363619534575013):
0.00000363619534575013,134_Layer14_K6_9:0.00000363619534575013):
0.00000363619534575013,
(145_layer16_M7_16:0.00132774593050852567,132_layer14_K7_9:0.00000363619534575013):
0.00133713032142029464):0.00278647994986401396,
(136_layer14_D7_16:0.00000363619534575013,130_12_M4_6_Haplo:
0.00131994653001272968):0.00141651841126976832):
0.00125910185854779654):0.00403005260407361416,
((62_layer12_M4_5:0.00126937068342301146,
((86_layer12_M4D_6:0.00128584289693581526,
(73_layer12_M4D_6:0.00128363904623272625,57_12_M4_5_Haplo:
0.00000363619534575013):0.00000363619534575013):0.00000363619534575013,
(((66_layer12_M4_5:0.00128838377089412386,54_12_M4_5_Haplo:
0.00128853886813459946):0.00000363619534575013,
(((65_layer12_M4_5:0.00128884461869839973,71_layer12_M4D_6:0.00000363619534575013):
0.00000363619534575013,46_layer12_M3_9:0.00000363619534575013):
0.00000363619534575013,56_12_M4_5_Haplo:0.00000363619534575013):
0.00000363619534575013):
0.00000363619534575013,80_layer12_M4D_6:0.00129274952360672085):
0.00128747536906372701):0.00130570538219615829):0.00817091584735905874,
(49_layer12_M3_1:0.00256999670460223003,(((((D_torquatus_E_Kolyma:
0.00120531358297111383,D_torquatus_E_Kolyma3:0.00000363619534575013):
0.00771015462378700587,D_torquatus_E_Kolyma2:0.00497959377899245825):
0.00395369005417124230,79_layer12_M4D_6:0.00124108783173599549):
0.00000363619534575013,(126_layer12_M3_2:0.00125541203451745163,
(51_layer12_M3_1:0.00000363619534575013,128_12_M3_2_Haplo:
0.00000363619534575013):0.00000363619534575013):
0.00124131096933333888):0.00000363619534575013,(((D_torquatus_Taymyr:
0.00000363619534575013,D_torquatus_Taymyr2:0.00000363619534575013):
0.00517034449906722277,((D_torquatus_Yamal:0.00265788371535682563,
(D_torquatus_Pechora:0.00260245233305352475,D_torquatus_Kanin:
0.00522030069062469609):0.00128598315030102996):0.00128459424545687923,
(150_UK_Yngr_dryas:0.00520455735781596464,(149_UK_dryas_Haplo:
0.00125427769367385147,153_UK_Yngr_dryas:0.00000363619534575013):
0.00000363619534575013):0.00000363619534575013):
0.00000363619534575013):0.00127745439282606044,(D_torquatus_W_Kolyma:
0.00259264052177891153,D_torquatus_Olenski:0.00122822421295203338):
0.00261310670036057598):0.00124373314667413411):
0.00000363619534575013):0.00403594532436997271):
0.00106724494576406663):0.00266572786165118845,
((E026:0.00206182631963185582,
(E036:0.00000363619534575013,E014:0.00262369135172486109):
0.00185264307150822920):0.00258387553564366377,
(((E019:0.00131795249856911140,((E049:0.00267010389584985573,
(E029:0.00000363619534575013,(E051:0.00844430881099344881,
(E050:0.00142855263970429001,
((E020:0.00144999712504058635,E027:0.00983731550324775349):
0.00539467881618129093,
(E052:0.00264611972331375844,E024:0.00000363619534575013):
0.00000363619534575013):0.00411087587953217360):
0.00278091458703202867):0.00130152933468939518):
0.00135011154385100045):
0.00131564916088999112,E018:0.00000363619534575013):
0.00000363619534575013):
0.00130834356062447198,E023:0.00000363619534575013):
0.00000363619534575013,
((144_layer16_C7_19:0.01276570132063204431,E015:0.00866622710162602734):
0.00567997135407338500,E012:0.00234361438279412837):
0.00165979415839065956):0.00761133019019519068):
0.00198464714858766602):0.02682618930035064048,D_hudsonius_b:
0.02682618930035064048);
bipartition tree:
((((((48_layer12_M3_9:0.00000363619534575013,
(47_layer12_M3_9:0.00129942266970888877,131_layer12_M4_6:0.00131404211215039321)16:0.00000363619534575013)65:0.00132730118271114994,E047:0.00130513155135699973)64:0.00134846575657471333,
((((133_layer14_K6_9:0.00134145769075794011,
(135_layer14_D7_16:0.00271945986349485073,
(129_layer12_M4_6:0.00546163750744719286,146_layer16_M7_16:0.00000363619534575013)47:0.00133568851414785777)17:0.00000363619534575013)4:0.00000363619534575013,134_Layer14_K6_9:0.00000363619534575013)12:0.00000363619534575013,
(145_layer16_M7_16:0.00132774593050852567,132_layer14_K7_9:0.00000363619534575013)68:0.00133713032142029464)85:0.00278647994986401396,
(136_layer14_D7_16:0.00000363619534575013,130_12_M4_6_Haplo:
0.00131994653001272968)58:0.00141651841126976832)57:0.00125910185854779654)78:0.00403005260407361416,
((62_layer12_M4_5:0.00126937068342301146,
((86_layer12_M4D_6:0.00128584289693581526,
(73_layer12_M4D_6:0.00128363904623272625,57_12_M4_5_Haplo:
0.00000363619534575013)19:0.00000363619534575013)26:0.00000363619534575013,
(((66_layer12_M4_5:0.00128838377089412386,54_12_M4_5_Haplo:
0.00128853886813459946)7:0.00000363619534575013,
(((65_layer12_M4_5:0.00128884461869839973,71_layer12_M4D_6:0.00000363619534575013)52:0.00000363619534575013,46_layer12_M3_9:0.00000363619534575013)4:0.00000363619534575013,56_12_M4_5_Haplo:
0.00000363619534575013)8:0.00000363619534575013)12:0.00000363619534575013,80_layer12_M4D_6:0.00129274952360672085)26:0.00128747536906372701)38:0.00130570538219615829)76:0.00817091584735905874,
(49_layer12_M3_1:0.00256999670460223003,(((((D_torquatus_E_Kolyma:
0.00120531358297111383,D_torquatus_E_Kolyma3:0.00000363619534575013)100:0.00771015462378700587,D_torquatus_E_Kolyma2:0.00497959377899245825)61:0.00395369005417124230,79_layer12_M4D_6:0.00124108783173599549)11:0.00000363619534575013,
(126_layer12_M3_2:0.00125541203451745163,
(51_layer12_M3_1:0.00000363619534575013,128_12_M3_2_Haplo:
0.00000363619534575013)56:0.00000363619534575013)65:0.00124131096933333888)5:0.00000363619534575013,
(((D_torquatus_Taymyr:
0.00000363619534575013,D_torquatus_Taymyr2:0.00000363619534575013)99:0.00517034449906722277,
((D_torquatus_Yamal:0.00265788371535682563,(D_torquatus_Pechora:
0.00260245233305352475,D_torquatus_Kanin:
0.00522030069062469609)67:0.00128598315030102996)61:0.00128459424545687923,
(150_UK_Yngr_dryas:0.00520455735781596464,(149_UK_dryas_Haplo:
0.00125427769367385147,153_UK_Yngr_dryas:
0.00000363619534575013)73:0.00000363619534575013)26:0.00000363619534575013)8:0.00000363619534575013)31:0.00127745439282606044,
(D_torquatus_W_Kolyma:0.00259264052177891153,D_torquatus_Olenski:
0.00122822421295203338)73:0.00261310670036057598)35:0.00124373314667413411)11:0.00000363619534575013)66:0.00403594532436997271)24:0.00106724494576406663)33:0.00266572786165118845,
((E026:0.00206182631963185582,
(E036:0.00000363619534575013,E014:0.00262369135172486109)68:0.00185264307150822920)52:0.00258387553564366377,
(((E019:0.00131795249856911140,((E049:0.00267010389584985573,
(E029:0.00000363619534575013,(E051:0.00844430881099344881,
(E050:0.00142855263970429001,
((E020:0.00144999712504058635,E027:0.00983731550324775349)83:0.00539467881618129093,
(E052:0.00264611972331375844,E024:0.00000363619534575013)34:0.00000363619534575013)64:0.00411087587953217360)49:0.00278091458703202867)23:0.00130152933468939518)27:0.00135011154385100045)30:0.00131564916088999112,E018:0.00000363619534575013)4:0.00000363619534575013)17:0.00130834356062447198,E023:0.00000363619534575013)12:0.00000363619534575013,
((144_layer16_C7_19:0.01276570132063204431,E015:0.00866622710162602734)48:0.00567997135407338500,E012:0.00234361438279412837)22:0.00165979415839065956)75:0.00761133019019519068)62:0.00198464714858766602):
0.45000000000000001110,D_hudsonius_b:0.45000000000000001110);
Ingo Michalak
Nov 11, 2011, 12:04:41 PM11/11/11
to raxml
Hello Jess,
first you are missing a comma after your first taxon name in the
consensus tree, this is one part of the problem. An other part is,
that the consensus trees produced by RAxML follow the format
":length[support]", which is not supported in figtree (and maybe also
in treeedit?). Dendroscope and Treeview should be able to open these
files, though. If you prefer figtree (like I do), you can use a work
around:
open the consensus treefile in a text editor that is able to handle
regular expressions (I use on mac "textwrangler" and on pc "notepad+
+") and open the replace function and exchange every
([:]\d+[.]\d+)[[](\d+)[]]
for
\2\1
afterwards figtree is able to read your file.
Hope that helps
Ingo
first you are missing a comma after your first taxon name in the
consensus tree, this is one part of the problem. An other part is,
that the consensus trees produced by RAxML follow the format
":length[support]", which is not supported in figtree (and maybe also
in treeedit?). Dendroscope and Treeview should be able to open these
files, though. If you prefer figtree (like I do), you can use a work
around:
open the consensus treefile in a text editor that is able to handle
regular expressions (I use on mac "textwrangler" and on pc "notepad+
+") and open the replace function and exchange every
([:]\d+[.]\d+)[[](\d+)[]]
for
\2\1
afterwards figtree is able to read your file.
Hope that helps
Ingo
Alexis
Nov 14, 2011, 7:18:19 AM11/14/11
to raxml
Thanks Ingo,
What Ingo says is all correct and should help to resolve your problem.
Alexis
> ...
>
> Erfahren Sie mehr »
What Ingo says is all correct and should help to resolve your problem.
Alexis
>
> Erfahren Sie mehr »
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