Thank you so much for your work with the Biobakery tools. The tools are very useful!
In am working with StrainPhlAn 3 and encountered a problem I hope you can help me solve.
The concatenated alignment file is quite short - I included two examples of this. E.g. for s__Akkermansia_muciniphila I have 52 markers available after filtering. However, in the concatenated alignment file the concatenated length for each sample is solely 5396 characters.
(for E. coli it is 27 markers and only 997 characters). You can see the output for the two species in the attached files.
I tried to change the --phylophlan_mode to “accurate” as I saw that using the default parameter only 500 nucleotides are included from each marker. However, this did not cause any difference.
I also updated both StrainPhlAn and PhyloPhlAn and likewise, this did not help.
I am worried that this will be too sparse information to obtain a meaningful phylogenetic reconstruction (if e.g. it is solely based on 997 nucleotides).
I can see from the output in the tutorial that you get 14355 characters pr. sample (for s__Eubacterium_rectale)
Hope you can help clarify my problem.
Kind regards Anne.
s__Escherichia_coli.StrainPhlAn3_concatenated.aln.txt (14.9 KB)
s__Escherichia_coli.info.txt (743 Bytes)
s__Akkermansia_muciniphila.StrainPhlAn3_concatenated.aln.txt (63.4 KB)
s__Akkermansia_muciniphila.info.txt (751 Bytes)