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Introduced the possibility it could be population genetics, which is a different calculation
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M__ ♦
M__ ♦
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Can you give a little more information about what tools and data sets you are using? How did you generate the OTU table etc?

If the underlying data is nucleotide data and this is a phylogentic tree. It may well be a population genetic tree based for example in allele frequencies.

For classical phylogenetics then FastTree is a very simple tool to generate a decent phylogeny. If you have the sequences of each OTU, you can align them in MegaX with muscle, or simply using muscle from the command line if you prefer. You can then generate the tree with this command (presuming you are on windows):

FastTree.exe -gtr -nt < aligned_sequences.fasta > otus_tree.tre

I hope that helps!

Can you give a little more information about what tools you are using? How did you generate the OTU table etc?

FastTree is a very simple tool to generate a decent phylogeny. If you have the sequences of each OTU, you can align them in MegaX with muscle, or simply using muscle from the command line if you prefer. You can then generate the tree with this command (presuming you are on windows):

FastTree.exe -gtr -nt < aligned_sequences.fasta > otus_tree.tre

I hope that helps!

Can you give a little more information about what tools and data sets you are using? How did you generate the OTU table etc?

If the underlying data is nucleotide data and this is a phylogentic tree. It may well be a population genetic tree based for example in allele frequencies.

For classical phylogenetics then FastTree is a very simple tool to generate a decent phylogeny. If you have the sequences of each OTU, you can align them in MegaX with muscle, or simply using muscle from the command line if you prefer. You can then generate the tree with this command (presuming you are on windows):

FastTree.exe -gtr -nt < aligned_sequences.fasta > otus_tree.tre

I hope that helps!

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adamsorbie
adamsorbie
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Can you give a little more information about what tools you are using? How did you generate the OTU table etc?

FastTree is a very simple tool to generate a decent phylogeny. If you have the sequences of each OTU, you can align them in MegaX with muscle, or simply using muscle from the command line if you prefer. You can then generate the tree with this command (presuming you are on windows):

FastTree.exe -gtr -nt < aligned_sequences.fasta > otus_tree.tre

I hope that helps!