How draw Phylogeny tree using genotype file?
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21 months ago
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I like to draw a phylogenetic tree for some samples based on SNP regions and genotype for each sample, I used 'SNPhylo' but it couldnt help me because I only have 90 SNP regions and I got error based on 'SNPhylo'. I would like to know is there any way to draw a nice tree based on the data that I have?

Data:

    ID  REF   alleles   gt  gt_0    gt_1    gt_2    gt_3    gt_4
rs10168838  T   G,T,    GG    GG      GG      GG      GG    GG
rs10209944  A   A,G,    GG    GG      GG      GG      GG    GG
rs1115049   A   A,G,    GG    GG      GG      GG      GG    GG
rs1115050   A   A,C,    CC    CC      CC      CC      CC    CC
rs13014347  T   C,T,    CC    CC      CC      CC      CC    CC
rs1517402   A   A,T,    TT    TT      TT      TT      TT    TT
rs1529408   G   G,T,    GT    TT      TT      TT      TT    GT
rs1545121   G   A,G,    AA    AA      AA      AA      AA    AA
rs1561247   C   C,T,    TT    TT      TT      TT      TT    TT
rs1809028   A   A,G,    AG    AG      GG      GG      GG    GG
rs1863812   T   C,T,    TC    CC      CC      CC      CC    TC
rs2072447   G   C,G,    CC    CC      CC      GC      CC    CC
rs2075221   C   C,G,T,  TT    TT      TT      TT      TT    CT
rs2286238   T   C,T,    CC    CC      CC      CC      CC    TC
rs2303599   C   C,T,    CT    TT      TT      TT      TT    TT
rs2303604   A   A,T,    AT    TT      TT      TT      TT    AT
rs2305155   A   A,G,    AG    GG      GG      GG      GG    GG
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phylogenic_tree Tree R Phylogenetic • 465 views
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Entering edit mode
21 months ago

Try using MEGA X but I think you're gonna have to convert your data into a MEGA-compatible format (usually ends with a '.meg' extension).