insert_seqs_into_tree.py – Tree Insertion¶
Description:
This script takes a set of aligned sequences (query) either in the same file as the aligned reference set or separated (depending on method) along with a starting tree and produces a new tree containing the query sequences. This script requires that the user is running Raxml v7.3.0, PPlacer git repository version and ParsInsert 1.0.4.
Usage: insert_seqs_into_tree.py [options]
Input Arguments:
Note
[REQUIRED]
- -i, --input_fasta_fp
- Path to the input fasta file
- -o, --output_dir
- Path to the output directory
- -t, --starting_tree_fp
- Starting Tree which you would like to insert into.
- -r, --refseq_fp
- Filepath for reference alignment
[OPTIONAL]
- -m, --insertion_method
- Method for aligning sequences. Valid choices are: pplacer, raxml_v730, parsinsert [default: raxml_v730]
- -s, --stats_fp
- Stats file produced by tree-building software. REQUIRED if -m pplacer [default: None]
- -p, --method_params_fp
- Parameters file containing method-specific parameters to use. Lines should be formatted as ‘raxml:-m GTRCAT’ (note this is not a standard QIIME parameters file, but a RAxML parameters file). [default: None]
Output:
The result of this script produces a tree file (in Newick format) along with a log file containing the output from the underlying tool used for tree insertion.
RAxML Example (default):
If you just want to use the default options, you can supply an alignment files where the query and reference sequences are included, along with a starting tree as follows:
insert_seqs_into_tree.py -i aligned_query_seqs.fasta -r aligned_reference_seqs.fasta -t starting_tree.tre -o insertion_results
ParsInsert Example:
If you want to insert sequences using pplacer, you can supply a fasta file containg query sequences (aligned to reference sequences) along with the reference alignment, a starting tree and the stats file produced when building the starting tree via pplacer as follows:
insert_seqs_into_tree.py -i aligned_query_seqs.fasta -r aligned_reference_seqs.fasta -t starting_tree.tre -o insertion_results -m parsinsert
Pplacer Example:
If you want to insert sequences using pplacer, you can supply a fasta file containg query sequences (aligned to reference sequences) along with the reference alignment, a starting tree and the stats file produced when building the starting tree via pplacer as follows:
insert_seqs_into_tree.py -i aligned_query_seqs.fasta -r aligned_reference_seqs.fasta -t starting_tree.tre -o insertion_results -m pplacer
Parameters file:
Additionally, users can supply a parameters file to change the options of the underlying tools as follows:
insert_seqs_into_tree.py -i aligned_query_seqs.fasta -r aligned_reference_seqs.fasta -t starting_tree.tre -o insertion_results -p raxml_parameters.txt