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. [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