04 advanced analyses

hierarchical taxonomic updating - different number of OTU per rank:

Update an alignment with different settings of mrca, sampling threshold and downtorank settings.

There is an example file in example_setups: 04_example_different_rank_sampling.py.

add unpublished data

Instead of using GenBank as the source of new sequences, we can specify a folder that contains sequences in fasta format and this folder will be used as a sequence database. Before using the BLAST database to find new sequences, sequences from that folder can be added to the alignment/phylogeny if the folder contains sequences that are similar to the sequences already present in the alignment. This is intended to be used for newly sequenced material, which is not yet published on GenBank. To use this you need to adapt the unpublished sequence settings.

There is an example file in ./example_setups/03_example_aln_addunpublishedsequences.py. An example on how the local database needs to look is provided in ./data/unpublished_seqs and for the naming of the samples see ./data/unpublished_names.csv.