Adrian Viehweger

So this means one would overestimate the number of present genomes in a given metagenomic sample, in the case of OGRE?

I just sent it.

Odd. When I run `muscle` followed by `FastTree` manually and proceed w/ the following step in the tutorial ```bash anvi-interactive --tree phylogenomic-tree.txt \ -p temp-profile.db \ --title "Pylogenomics of IGD...

Sure: ```bash anvi-gen-phylogenomic-tree -f seqs-for-phylogenomics.fa -o phylogenomic-tree.txt --debug Input aligment file path .....................: .../gone-fishing/INFANT-GUT-TUTORIAL/seqs-for-phylogenomics.fa Output file path .............................: .../gone-fishing/INFANT-GUT-TUTORIAL/phylogenomic-tree.txt Alignment names ..............................: P_avidum, F_magna, L_citreum, S_aureus, Aneorococcus_sp, Streptococcus, S_epidermidis, C_albicans,...

Further testing gives me the impression that (1) this does not always occur given the same input and (2) only occured when I add the --confidence flag to treetime.

Yes, this is a larger tree (20+ leaves) but 3 of them are identical in their SNV alignment, but the dates are different. Is there a way around this instability,...

which data do you need? the alignment, dates, undated tree -- anything else?

[root_to_tip_regression.pdf](https://github.com/neherlab/treetime/files/5181340/root_to_tip_regression.pdf)

I really appreciate this, thank you.

There's a nice syntax documentation: https://www.rosettacommons.org/docs/latest/rosetta_basics/file_types/resfiles