pplacer-SCAMPP is an extension for the maximum likelihood phylogenetic placement method pplacer, which allows pplacer to run on ultra-large reference trees.
Similarly EPA-ng-SCAMPP is an extension of EPA-ng, allowing it to run on ultra-large reference trees.
They are both python programs that can be run on Linux and MacOS
- Python: Version >= 3.0
- Treeswift
- pplacer: Version 1.1.alpha19 (for pplacer-SCAMPP) or EPA-ng: Version 0.3.8 (for EPA-ng-SCAMPP)
The input parameters for pplacer-SCAMPP and EPA-ng-SCAMPP are as follows:
Required arguments:
-i, --info : statistics file path produced by RAxML version 7 for pplacer-SCAMPP or RAxML-ng for EPA-ng-SCAMPP containing the substitution rates
-t, --tree : reference tree file path (in newick format) (parameter T)
-d, --outdir : directory to where output file pplacer-SCAMPP.jplace is written
-a, --alignment : fasta format file path containing the multiple sequence alignment (MSA) of reference and query sequences (parameter A) (query sequences optional if aligned queries are in given with -q option in a separate file)
Optional arguments:
-m, --model : DNA substitution model such as GTR for nucleotides
-q, --qalignment : file containing a list of query sequences aligned to the reference MSA in fasta format (needed when not contained in file with reference MSA)
-b, --subtreesize : maximum size of the subtree for placement (with pplacer 2000 is recommended, and with EPA-ng 10,000 is recommended) (parameter B)
-s, --subtreetype : options for collecting nodes for the subtree - d (default) for edge weighted distances, n for node distances, h for Hamming distances
-n, --tmpfilenbr : number for working directories in the current file path (to allow to run multiple instances concurently)
-f, --fragmentflag : boolean, True is you wish to mask leading and trailing gaps in each query sequence when finding closest sister taxon.
Usage: Please run from a directory containing the respective phylogenetic placement method. This would be pplacer (available at https://github.com/matsen/pplacer) for pplacer-SCAMPP or EPA-ng (available at https://github.com/Pbdas/epa-ng) for EPA-ng-SCAMPP.
python3 pplacer-SCAMPP.py -i INFO -t TREE -d OUTDIR -a ALIGNMENT
python3 EPA-ng-SCAMPP.py -i INFO -t TREE -d OUTDIR -a ALIGNMENT