How to create a .phy file for constructing a phylogenetic tree?

Python works great for tying everything together and file manipulations. I find stepping out of Python, using system calls, best for alignment and tree building. For example:

os.system("mafft --auto {} > {}" .format("unaligned_16s_seq_in_file.fasta", "alignment_out_file.fasta"))

os.system("raxml -f a -s {} -p 12345 -x 12345 -# 100 -m GTRCAT -n {}" .format("alignment_out_file.fasta", "tree_out_file.tre"))

Dipesh Nepal Follow

Python works great for tying everything together and file manipulations. I find stepping out of Python, using system calls, best for alignment and tree building. For example:

os.system("mafft --auto {} > {}" .format("unaligned_16s_seq_in_file.fasta", "alignment_out_file.fasta"))os.system("raxml -f a -s {} -p 12345 -x 12345 -# 100 -m GTRCAT -n {}" .format("alignment_out_file.fasta", "tree_out_file.tre"))

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David Curran Follow

You simply use Biopython's SeqIO and AlignIO.The documentation is https://biopython.org/wiki/AlignIO etc ...The format you seek is phylip

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Josh-D. Davis Follow

, I got "ValueError: Sequences must all be the same length". I'm not sure why, because I explicitly checked that the sequences have the same length. Not sure what to do now :( Any thoughts?More

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Jim McElhinney Follow

Possibly it is not a programming issue but formating. There is no simple answer to trouble shoot this. Could you ask this as a separate question please? Obviously it is solvable but there's several possibilities and the Moderators will intervene if there are multiple questions within a threadMore

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