phylogenetic tree + AA susbtitution + belgium chocolate
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joaopaulo catani
Oct 14, 2020, 9:15:49 AM10/14/20
to ggtree
Dear ggtree community,
Error in read.phyDat(tipseqfile, format = "fasta") :
sequences have different length
> fit <- pml(tre, tipseq, k=4)
Error in pml(tre, tipseq, k = 4) : object 'tipseq' not found
> fit <- optim.pml(fit, optNni=FALSE, optBf=T, optQ=T,
+ optInv=T, optGamma=T, optEdge=TRUE,
+ optRooted=FALSE, model = "GTR",
+ control = pml.control(trace =0))
Error in optim.pml(fit, optNni = FALSE, optBf = T, optQ = T, optInv = T, :
object 'fit' not found
> pmltree <- as.treedata(fit)
Error in as.treedata(fit) : object 'fit' not found
> ggtree(pmltree) + geom_text(aes(x=branch, label=AA_subs, vjust=-.5))
Error in ggplot(tr, mapping = mapping, layout = layout, mrsd = mrsd, as.Date = as.Date, :
object 'pmltree' not found
I would like to plott its
phylogenetic tree including the amino acid changes in the branches (as
in the figure 1.4 in the book of Prof.Yu). I am using a nwk tree first
generated in CLC software and them the fasta alignment of those proteins
as the following:
library(phangorn)
library(treeio)
library(ggtree)
#parsing the data
treefile <- system.file("work", "NA.nwk", package="treeio")
tre <- read.tree(treefile)
tipseqfile <- system.file("work", "NA.fa", package="treeio")
tipseq <- read.phyDat(tipseqfile,format="fasta")
fit <- pml(tre, tipseq, k=4)
fit <- optim.pml(fit, optNni=FALSE, optBf=T, optQ=T,
optInv=T, optGamma=T, optEdge=TRUE,
optRooted=FALSE, model = "GTR",
control = pml.control(trace =0))
pmltree <- as.treedata(fit)
ggtree(pmltree) + geom_text(aes(x=branch, label=AA_subs, vjust=-.5))
library(treeio)
library(ggtree)
#parsing the data
treefile <- system.file("work", "NA.nwk", package="treeio")
tre <- read.tree(treefile)
tipseqfile <- system.file("work", "NA.fa", package="treeio")
tipseq <- read.phyDat(tipseqfile,format="fasta")
fit <- pml(tre, tipseq, k=4)
fit <- optim.pml(fit, optNni=FALSE, optBf=T, optQ=T,
optInv=T, optGamma=T, optEdge=TRUE,
optRooted=FALSE, model = "GTR",
control = pml.control(trace =0))
pmltree <- as.treedata(fit)
ggtree(pmltree) + geom_text(aes(x=branch, label=AA_subs, vjust=-.5))
I got no tree and the following error:
Error in read.phyDat(tipseqfile, format = "fasta") :
sequences have different length
> fit <- pml(tre, tipseq, k=4)
Error in pml(tre, tipseq, k = 4) : object 'tipseq' not found
> fit <- optim.pml(fit, optNni=FALSE, optBf=T, optQ=T,
+ optInv=T, optGamma=T, optEdge=TRUE,
+ optRooted=FALSE, model = "GTR",
+ control = pml.control(trace =0))
Error in optim.pml(fit, optNni = FALSE, optBf = T, optQ = T, optInv = T, :
object 'fit' not found
> pmltree <- as.treedata(fit)
Error in as.treedata(fit) : object 'fit' not found
> ggtree(pmltree) + geom_text(aes(x=branch, label=AA_subs, vjust=-.5))
Error in ggplot(tr, mapping = mapping, layout = layout, mrsd = mrsd, as.Date = as.Date, :
object 'pmltree' not found
Could
someone help me to add those AA substitutions to that tree? I will be
happy to send you a chocolate from Belgium as a well deserved prize.
Thank you.
Kind regards
JP
joaopaulo catani
Oct 14, 2020, 10:45:53 AM10/14/20
to ggtree
That is the tree:
('(B_Lee_1940)':0.04738200681663222,(((((((('(B_Sichuan_379_99)':0.002491907253036801,'(B_Shanghai_361_2002)':0.006459984796158746)50:7.735270641650541E-13,'(B_Victoria_504_2000)':0.006115003594842397)81:2.3274415067201746E-14,'(B_Malaysia_2506_2004)':0.019164175712188942)30:0.008968535505371912,(('(B_Harbin_7_1994)':5.71846215952964E-14,'(B_Beijing_184_93)':0.010790653436740082)61:0.004300361800762661,('(B_Yamanashi_166_1998)':0.002148592359039275,'(B_Memphis_12_97)':0.002148590845106728)97:0.008626745773710568)24:7.034632918380034E-13)19:3.534092886113052E-14,(('(B_Utah_09_2014)':0.012963576672788009,'(B_Wisconsin_01_2010)':7.7089950615051355E-16)59:0.005279835547390347,'(B_Florida_04_2006)':0.010183987577081393)85:0.016965562406693967)15:0.002399718053491727,'(B_Yamagata_16_1988)':0.02584899515082787)27:7.695175670973794E-13,(('(B_Washington_02_2019)':0.00214859379826665,'(B_Colorado_06_2017)':0.00214859381276687)99:0.01038827634786369,'(B_Brisbane_60_2008)':0.002675064086340904)91:0.035747120599952394)82:0.024144373228555047,(('(B_Victoria_02_1987)':0.012901519490400163,'(B_Shangdong_7_97)':0.010842808448117233)51:4.752640803316321E-13,'(B_Hong':0.013031447746011596)84:0.009266983682318904):0.015237091298205392):0.0;
And those are the AA sequences:
>(B_Hong/1-466 Kong/330/2001)
MLPSTIQTLTLFLTSGGVLLSLYVSALLSYLLYSDILLKFSPTKIIAPTTSLDSANASNFQAVNHSATKEMT
FLLPEPEWTYPRLSCQGSTFQKALLISPHRFGEAKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVNLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALIKIKYGEAYTDTYHS
YANNILRTQESACNCIGGDCYLMITDGSASGISKCRFLKIREGRIVKEIFPTGRVEHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGSGGIKGGFVHQRMASK
IGRWYSRTMSKTKRMGMELYVKYDGDPWTDSDALAPSGVMVSIEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKTTWHSAATAIYCLMGSGQLLWDTITGVDMAL
>(B_Shangdong_7_97)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSALLSYLLYSDILLKFSPTKVIAPTMSLDCANASNVQAVNHSATEEMT
FLLPEPEWTYPRLSCQGSTFQKALLISPHRFGEAKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVNLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALIKIKYGEAYTDTYHS
YANNILRTQESACNCIGGDCYLMITDGSASGISRCRFLKIREGRIIKEIFPTGRVEHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGNGGIKGGFVHQRMASR
IGRWYSRTMSKTKRMGMELYVKYDGDPWTDSDALAPSGVMVSIEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKKTWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Victoria_02_1987)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSALLSYLLYSDILLKFSPTKIIAPTMSLDCANASNVQAANHSATKEMT
FLLPEPEWTYPRLSCQGSTFQKALLISPHRFGEAKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVNLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALIKIKYGEAYTDTYHS
YANNILRTQESACNCIGGDCYLMITDGSASGISKCRFLKIREGRIIKEIFPTGRVEHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGEKGRGGIKGGFVHQRMASK
IGRWYSRTMSKTERMGMELYVKYDGDPWTDSDALAPSGVMVSMKEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKKTWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Brisbane_60_2008)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSPTEITAPTMPLDCANASNVQAVNRSATKGVT
LLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPNECKHFALTHYAAQPGGYYN
GTRGDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDNNALLKVKYGEAYTDTYHS
YANKILRTQESACNCIGGNCYLMITDGSASGVSECRFLKIREGRIIKEIFPTGRVKHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTDTYLDTPRPNDGSITGPCESNGDKGSGGIKGGFVHQRMESK
IGRWYSRTMSKTERMGMGLYVKYDGDPWADSDALAFSGVMVSMKEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKETWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Colorado_06_2017)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSPTEITAPTMPLDCANASNVQAVNRSATKGVT
LLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFVACGPNECKHFALTHYAAQPGGYYN
GTRGDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDNNALLKVKYGEAYTDTYHS
YANNILRTQESACNCIGGNCYLMITDGSASGVSECRFLKIREGRIIKEIFPTGRVKHTEECTCGFASNKTIE
CACRDNRYTAKRPFVKLNVETDTAEIRLMCTDTYLDTPRPNDGSITGPCESDGDKGSGGIKGGFVHQRMKSK
IGRWYSRTMSQTERMGMGLYVKYGGDPWADSDALAFSGVMVSMKEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKETWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Washington_02_2019)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSPTEITAPTMPLDCANASNVQAVNRSATKGVT
LLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFVACGPNECKHFALTHYAAQPGGYYN
GTRGDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDNNALLKVKYGEAYTDTYHS
YANNILRTQESACNCIGGNCYLMITDGSASGVSECRFLKIREGRIIKEIFPTGRVKHTEECTCGFASNKTIE
CACRDNRYTAKRPFVKLNVETDTAEIRLMCTDTYLDTPRPNDGSITGPCESDGDKGSGGIKGGFVHQRMKSK
IGRWYSRTMSKTERMGMGLYVKYGGDPWADSDALTFSGVMVSMKEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKETWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Yamagata_16_1988)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSPTEITAPKVPLDCANASNVQAVNRSATKGMT
LLLSEPEWTYPRLSCQGSTFQKALLISPHRFGETRGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALIKIKYGEAYTDTYHS
YANNILRTQESACNCIGGDCYLMITDGSASGISKCRFLKIREGRIIKEIFPTGRVEHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGRGGIKGGFVHQRMASK
IGRWYSRTMSKTERMGMELYVKYDGDPWTDSDALAPSGVMVSMKEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKKTWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Florida_04_2006)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSQTEITAPIMPLDCANASNVQAVNRSAAKGVT
LLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPTECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDSNALLKIKYGEAYTDTYHS
YAKNILRTQESACNCIGGDCYLMITDGPASGISECRFLKIREGRIIKEIFPTGRVKHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPNDGSITGPCESDGDKGSGGIKGGFVHQRMASK
IGRWYSRTMSKTKRMGMGLYVKYDGDPWTDSEALALSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKTTWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Wisconsin_01_2010)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSRTEITAPIMPLDCANASNVQAVNRSATKGVT
LLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALLKIKYGEAYTDTYHS
YAKNILRTQESACNCIGGDCYLMITDGPASGISECRFLKIREGRIIKEIFPTGRVKHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPNDGSITGPCESNGDKGSGGIKGGFVHQRMASK
IGRWYSRTMSKTKRMGMGLYVKYDGDPWTDSEALALSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKTTWHSAATAIYCLMGSGQLLWDTVTGVNMTL
>(B_Utah_09_2014)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSRTEVTAPIMPLDCANASNAQAVNRSATKGVT
PLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALLKIKYGEAYTDTYHS
YAKNILRTQESACNCIGGDCYLMITDGPASGISECRFLKIREGRIIKEIFPTGRVKHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTKTYLDTPRPNDGSITGPCESDGDEGSGGIKGGFVHQRMASK
IGRWYSRTMSKTKRMGMGLYVKYDGDPWTDSEALALSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKTTWHSAATAIYCLMGSGQLLWDTVTGVNMTL
>(B_Memphis_12_97)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSPTEITAPTMPLNCTNASNVQAVNRSATKGVT
LPLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALLKIKYGEAYTDTYHS
YANNILRTQESACNCIGGDCYLMITDGSASGISECRFLKIREGRIIKEIFPTGRVEHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGSGGIKGGFVHQRMASK
IGRWYSRTMSKTKRMGMGLYVKYDGDPWIDSDALTLSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKKTWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Yamanashi_166_1998)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSPTEITAPTMPLNCANASNVQAVNRSATKGVT
LPLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECRHFALTHYAAQPGGYYN
GTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALLKIKYGEAYTDTYHS
YANNILRTQESACNCIGGDCYLMITDGSASGISECRFLKIREGRIIKEIFPTGRVEHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGSGGIKGGFVHQRMASK
IGRWYSRTMSKTKRMGMGLYVKYDGDPWIDSDALTLSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKKTWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Beijing_184_93)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSPTEITAPTMPLDCANASNVQAVNRSATKGVT
LLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETRGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALLKIKYGEAYTDTYHS
YANNILRTQESACNCIGGDCYLMITDGSASGTSKCRFLKIREGRIIKEIFPTGRVEHTEECTCGFASNKTIE
CACRDNNYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGRGGIKGGFVHQRMASK
IGRWYSRTMSKTERMGMELYVKYDGDPWTDSDALALSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKKTWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Harbin_7_1994)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSPTEITAPTMPLDCANASNVQAVNRSATKGVT
LLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETRGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALLKIKYGEAYTDTYHS
YANNILRTQESACNCIGGDCYLMITDGSASGISKCRFLKIREGRIIKEIFPTGRVEHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGSGGIKGGFVHQRMASK
IGRWYSRTMSKTKRMGMGLYVKYDGDPWTDSDALALSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKKTWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Malaysia_2506_2004)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFPSTEITAPTMPLDCANASNVQAVNRSATKGVT
LLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTRGDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDNNALLKIKYGEAYTDTYHS
YANNILRTQESACNCIGGNCYLMITDGSASGVSECRFLKIREGRIIKEIFPTGRIKHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGSGGIKGGFVHQRMASK
IGRWYSRTMSKTKRMGMGLYVKYDGDPWADSDALAFSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKETWHSAATAIYCLMGSGQLLWDTVTGVNMAL
>(B_Victoria_504_2000)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSSTEITAPTMPLDCANASNVQAVNRSATEGVT
LLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDSNALLKIKYGEAYTDTYHS
YANNILRTQESACNCIGGNCYLMITDGSASGISECRFLKIREGRIIKEIFPTGRVEHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGSGGIKGGFVHQRMASK
IGRWYSRTMSKTKRMGMGLYVKYDGDPWTDSDALALSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKETWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Shanghai_361_2002)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSTTEITAPTMPLDCANASNVQAVNRSATKGVT
LLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDSNALLKIKYGEAYTDTYHS
YANNILRTQESACNCIGGNCYLMITDGSASGISECRFLKIREGRIIKEIFPTGRVKHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGNKGSGGIKGGFVHQRMASK
IGRWYSRTMSKTKRMGMGLYVKYDGDPWIDSDALALSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKETWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Sichuan_379_99)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSPTEITAPTMPLDCANASNVQAVNRSATKGVT
FLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDSNALLKIKYGEAYTDTYHS
YANNILRTQESACNCIGGNCYLMITDGSASGISECRFLKIREGRIIKEIFPTGRVKHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGSGGIKGGFVHQRMASK
IGRWYSRTMSKTKRMGMGLYVKYDGDPWTDSDALALSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKETWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Lee_1940)/1-466
MLPSTVQTLTLLLTSGGVLLSLYVSASLSYLLYSDVLLKFSSTKTTAPTMSLECTNASNAQTVNHSATKEMT
FPPPEPEWTYPRLSCQGSTFQKALLISPHRFGEIKGNSAPLIIREPFVACGPKECRHFALTHYAAQPGGYYN
GTRKDRNKLRHLVSVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDNDALVKIKYGEAYTDTYHS
YAHNILRTQESACNCIGGDCYLMITDGSASGISKCRFLKIREGRIIKEILPTGRVEHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTKTYLDTPRPDDGSIAGPCESNGDKWLGGIKGGFVHQRMASK
IGRWYSRTMSKTNRMGMELYVKYDGDPWTDSDALTLSGVMVSIEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKDTWHSAATAIYCLMGSGQLLWDTVTGVDMAL
MLPSTIQTLTLFLTSGGVLLSLYVSALLSYLLYSDILLKFSPTKIIAPTTSLDSANASNFQAVNHSATKEMT
FLLPEPEWTYPRLSCQGSTFQKALLISPHRFGEAKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVNLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALIKIKYGEAYTDTYHS
YANNILRTQESACNCIGGDCYLMITDGSASGISKCRFLKIREGRIVKEIFPTGRVEHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGSGGIKGGFVHQRMASK
IGRWYSRTMSKTKRMGMELYVKYDGDPWTDSDALAPSGVMVSIEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKTTWHSAATAIYCLMGSGQLLWDTITGVDMAL
>(B_Shangdong_7_97)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSALLSYLLYSDILLKFSPTKVIAPTMSLDCANASNVQAVNHSATEEMT
FLLPEPEWTYPRLSCQGSTFQKALLISPHRFGEAKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVNLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALIKIKYGEAYTDTYHS
YANNILRTQESACNCIGGDCYLMITDGSASGISRCRFLKIREGRIIKEIFPTGRVEHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGNGGIKGGFVHQRMASR
IGRWYSRTMSKTKRMGMELYVKYDGDPWTDSDALAPSGVMVSIEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKKTWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Victoria_02_1987)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSALLSYLLYSDILLKFSPTKIIAPTMSLDCANASNVQAANHSATKEMT
FLLPEPEWTYPRLSCQGSTFQKALLISPHRFGEAKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVNLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALIKIKYGEAYTDTYHS
YANNILRTQESACNCIGGDCYLMITDGSASGISKCRFLKIREGRIIKEIFPTGRVEHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGEKGRGGIKGGFVHQRMASK
IGRWYSRTMSKTERMGMELYVKYDGDPWTDSDALAPSGVMVSMKEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKKTWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Brisbane_60_2008)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSPTEITAPTMPLDCANASNVQAVNRSATKGVT
LLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPNECKHFALTHYAAQPGGYYN
GTRGDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDNNALLKVKYGEAYTDTYHS
YANKILRTQESACNCIGGNCYLMITDGSASGVSECRFLKIREGRIIKEIFPTGRVKHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTDTYLDTPRPNDGSITGPCESNGDKGSGGIKGGFVHQRMESK
IGRWYSRTMSKTERMGMGLYVKYDGDPWADSDALAFSGVMVSMKEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKETWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Colorado_06_2017)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSPTEITAPTMPLDCANASNVQAVNRSATKGVT
LLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFVACGPNECKHFALTHYAAQPGGYYN
GTRGDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDNNALLKVKYGEAYTDTYHS
YANNILRTQESACNCIGGNCYLMITDGSASGVSECRFLKIREGRIIKEIFPTGRVKHTEECTCGFASNKTIE
CACRDNRYTAKRPFVKLNVETDTAEIRLMCTDTYLDTPRPNDGSITGPCESDGDKGSGGIKGGFVHQRMKSK
IGRWYSRTMSQTERMGMGLYVKYGGDPWADSDALAFSGVMVSMKEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKETWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Washington_02_2019)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSPTEITAPTMPLDCANASNVQAVNRSATKGVT
LLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFVACGPNECKHFALTHYAAQPGGYYN
GTRGDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDNNALLKVKYGEAYTDTYHS
YANNILRTQESACNCIGGNCYLMITDGSASGVSECRFLKIREGRIIKEIFPTGRVKHTEECTCGFASNKTIE
CACRDNRYTAKRPFVKLNVETDTAEIRLMCTDTYLDTPRPNDGSITGPCESDGDKGSGGIKGGFVHQRMKSK
IGRWYSRTMSKTERMGMGLYVKYGGDPWADSDALTFSGVMVSMKEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKETWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Yamagata_16_1988)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSPTEITAPKVPLDCANASNVQAVNRSATKGMT
LLLSEPEWTYPRLSCQGSTFQKALLISPHRFGETRGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALIKIKYGEAYTDTYHS
YANNILRTQESACNCIGGDCYLMITDGSASGISKCRFLKIREGRIIKEIFPTGRVEHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGRGGIKGGFVHQRMASK
IGRWYSRTMSKTERMGMELYVKYDGDPWTDSDALAPSGVMVSMKEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKKTWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Florida_04_2006)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSQTEITAPIMPLDCANASNVQAVNRSAAKGVT
LLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPTECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDSNALLKIKYGEAYTDTYHS
YAKNILRTQESACNCIGGDCYLMITDGPASGISECRFLKIREGRIIKEIFPTGRVKHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPNDGSITGPCESDGDKGSGGIKGGFVHQRMASK
IGRWYSRTMSKTKRMGMGLYVKYDGDPWTDSEALALSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKTTWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Wisconsin_01_2010)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSRTEITAPIMPLDCANASNVQAVNRSATKGVT
LLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALLKIKYGEAYTDTYHS
YAKNILRTQESACNCIGGDCYLMITDGPASGISECRFLKIREGRIIKEIFPTGRVKHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPNDGSITGPCESNGDKGSGGIKGGFVHQRMASK
IGRWYSRTMSKTKRMGMGLYVKYDGDPWTDSEALALSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKTTWHSAATAIYCLMGSGQLLWDTVTGVNMTL
>(B_Utah_09_2014)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSRTEVTAPIMPLDCANASNAQAVNRSATKGVT
PLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALLKIKYGEAYTDTYHS
YAKNILRTQESACNCIGGDCYLMITDGPASGISECRFLKIREGRIIKEIFPTGRVKHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTKTYLDTPRPNDGSITGPCESDGDEGSGGIKGGFVHQRMASK
IGRWYSRTMSKTKRMGMGLYVKYDGDPWTDSEALALSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKTTWHSAATAIYCLMGSGQLLWDTVTGVNMTL
>(B_Memphis_12_97)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSPTEITAPTMPLNCTNASNVQAVNRSATKGVT
LPLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALLKIKYGEAYTDTYHS
YANNILRTQESACNCIGGDCYLMITDGSASGISECRFLKIREGRIIKEIFPTGRVEHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGSGGIKGGFVHQRMASK
IGRWYSRTMSKTKRMGMGLYVKYDGDPWIDSDALTLSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKKTWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Yamanashi_166_1998)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSPTEITAPTMPLNCANASNVQAVNRSATKGVT
LPLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECRHFALTHYAAQPGGYYN
GTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALLKIKYGEAYTDTYHS
YANNILRTQESACNCIGGDCYLMITDGSASGISECRFLKIREGRIIKEIFPTGRVEHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGSGGIKGGFVHQRMASK
IGRWYSRTMSKTKRMGMGLYVKYDGDPWIDSDALTLSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKKTWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Beijing_184_93)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSPTEITAPTMPLDCANASNVQAVNRSATKGVT
LLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETRGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALLKIKYGEAYTDTYHS
YANNILRTQESACNCIGGDCYLMITDGSASGTSKCRFLKIREGRIIKEIFPTGRVEHTEECTCGFASNKTIE
CACRDNNYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGRGGIKGGFVHQRMASK
IGRWYSRTMSKTERMGMELYVKYDGDPWTDSDALALSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKKTWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Harbin_7_1994)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSPTEITAPTMPLDCANASNVQAVNRSATKGVT
LLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETRGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALLKIKYGEAYTDTYHS
YANNILRTQESACNCIGGDCYLMITDGSASGISKCRFLKIREGRIIKEIFPTGRVEHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGSGGIKGGFVHQRMASK
IGRWYSRTMSKTKRMGMGLYVKYDGDPWTDSDALALSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKKTWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Malaysia_2506_2004)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFPSTEITAPTMPLDCANASNVQAVNRSATKGVT
LLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTRGDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDNNALLKIKYGEAYTDTYHS
YANNILRTQESACNCIGGNCYLMITDGSASGVSECRFLKIREGRIIKEIFPTGRIKHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGSGGIKGGFVHQRMASK
IGRWYSRTMSKTKRMGMGLYVKYDGDPWADSDALAFSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKETWHSAATAIYCLMGSGQLLWDTVTGVNMAL
>(B_Victoria_504_2000)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSSTEITAPTMPLDCANASNVQAVNRSATEGVT
LLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDSNALLKIKYGEAYTDTYHS
YANNILRTQESACNCIGGNCYLMITDGSASGISECRFLKIREGRIIKEIFPTGRVEHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGSGGIKGGFVHQRMASK
IGRWYSRTMSKTKRMGMGLYVKYDGDPWTDSDALALSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKETWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Shanghai_361_2002)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSTTEITAPTMPLDCANASNVQAVNRSATKGVT
LLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDSNALLKIKYGEAYTDTYHS
YANNILRTQESACNCIGGNCYLMITDGSASGISECRFLKIREGRIIKEIFPTGRVKHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGNKGSGGIKGGFVHQRMASK
IGRWYSRTMSKTKRMGMGLYVKYDGDPWIDSDALALSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKETWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Sichuan_379_99)/1-466
MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSPTEITAPTMPLDCANASNVQAVNRSATKGVT
FLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYN
GTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDSNALLKIKYGEAYTDTYHS
YANNILRTQESACNCIGGNCYLMITDGSASGISECRFLKIREGRIIKEIFPTGRVKHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGSGGIKGGFVHQRMASK
IGRWYSRTMSKTKRMGMGLYVKYDGDPWTDSDALALSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKETWHSAATAIYCLMGSGQLLWDTVTGVDMAL
>(B_Lee_1940)/1-466
MLPSTVQTLTLLLTSGGVLLSLYVSASLSYLLYSDVLLKFSSTKTTAPTMSLECTNASNAQTVNHSATKEMT
FPPPEPEWTYPRLSCQGSTFQKALLISPHRFGEIKGNSAPLIIREPFVACGPKECRHFALTHYAAQPGGYYN
GTRKDRNKLRHLVSVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDNDALVKIKYGEAYTDTYHS
YAHNILRTQESACNCIGGDCYLMITDGSASGISKCRFLKIREGRIIKEILPTGRVEHTEECTCGFASNKTIE
CACRDNSYTAKRPFVKLNVETDTAEIRLMCTKTYLDTPRPDDGSIAGPCESNGDKWLGGIKGGFVHQRMASK
IGRWYSRTMSKTNRMGMELYVKYDGDPWTDSDALTLSGVMVSIEEPGWYSFGFEIKDKKCDVPCIGIEMVHD
GGKDTWHSAATAIYCLMGSGQLLWDTVTGVDMAL
Yu, Guangchuang
Oct 15, 2020, 3:49:13 AM10/15/20
to joaopaulo catani, ggtree
treefile <- system.file("work", "NA.nwk", package="treeio")
tre <- read.tree(treefile)
tipseqfile <- system.file("work", "NA.fa", package="treeio")
should change to something like:
treefile <- path_to_your_file
see my explanation here: https://yulab-smu.top/treedata-book/faq.html#faq-local-file
--
1. G Yu*. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics. 2020, 69:e96. https://doi.org/10.1002/cpbi.96
2. LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu*. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution. 2020, 37(2):599-603. http://dx.doi.org/10.1093/molbev/msz240
3. G Yu*, TTY Lam, H Zhu, Y Guan*. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution, 2018, 35(2):3041-3043. https://doi.org/10.1093/molbev/msy194
4. G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data, Methods in Ecology and Evolution, 2017, 8(1):28-36. https://doi.org/10.1111/2041-210X.12628
5. Book: https://yulab-smu.top/treedata-book/
---
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--
--~--~---------~--~----~------------~-------~--~----~
Guangchuang Yu PhD
Professor, Associate Director
Department of Bioinformatics
School of Basic Medical Sciences
Southern Medical University
Guangzhou, China
-~----------~----~----~----~------~----~------~--~---
joaopaulo catani
Oct 16, 2020, 11:16:29 AM10/16/20
to Yu, Guangchuang, ggtree
Dear Dr Yu Thank you for your attention,
Finally the problem was solved, it was not the path_to_my_file. I was using AA sequences instead of nucleotide sequences and pml was setted to GRT. I back translated the sequences and it runned perfectly...
Kind regards
João Paulo Portela Catani
joaopaulo catani
Oct 16, 2020, 11:25:08 AM10/16/20
to Yu, Guangchuang, ggtree
Ps. How (besides AA substitutions) can I also plot the lengths of the branches?
João Paulo Portela Catani
João Paulo Portela Catani
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