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.. _insert_seqs_into_tree:
.. index:: insert_seqs_into_tree.py
*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:** :file:`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
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