Eleanor Wedell, Improved Phylogenetic Placement Methods. MS Thesis, in preparation.
Thank you for using these datasets.
These RNAsim aligned fragmentary sequences were generated from the query sequences selected by Balaban et al. (2019) in their variable-size datasets (https://doi.org/10.5061/dryad.78nf7dq). They were created for use for phylogenetic placement with the multiple sequence alignments and backbone trees provided by Balaban et al. (2019).
The file structures included here also correspond with the data Balaban et al. (2020) provided.
Directories for five varying backbone tree sizes, shown as 5000, 10000, 50000, 100000, and 200000. These directory names are also used by Balaban et al. (2019), and indicate the size of the backbone tree included in their data.
Subdirectories for each replicate from the backbone tree size labelled 0 through 4. For the smaller four backbone tree sizes there are five replicates, and for the largest there is one replicate.
Each replicate contains 200 text files with one aligned query sequence fragment in fasta format.