A toolkit for working with phylogenetic data.
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Extract Clade Placements

Summary

Takes a jplace file and a mapping of the taxa of its reference tree to some clade names. It outputs a jplace file for each clade, where each file contains all Pqueries that fell into that clade.

This demo is located at

genesis/doc/demos/extract_clade_placements.cpp

Details

The program takes three input arguments in the following order:

  1. A jplace input file. The pqueries in this file are then split into different samples. Each such sample contains all pqueries whose placements are placed in a certain clade of the reference tree with more than a cutoff threshold of their accumulated likelihood weight.

    According to the jplace standard, each pquery can have multiple possible placement positions. Each position has a value like_weight_ratio, which can be interpreted as a measure of probability of how likely the placement belongs to the branch that it is attached to. The ratios for all branches of the tree thus sum up to 1.0.

    If more of this placement mass than the threshold is placed on the branches of a single clade of the tree, the according pquery is assigned to that clade. The threshold is hardcoded in this demo and set to 0.95 (but can be changed if needed, of course).

    It is possible that the placement algorithm (e.g., EPA or pplacer) did not output placements with low like_weight_ratios, depending on the selected options (see the respective manual for more details on how to change this). This means that the provided sum might be lower than 1.0 for some pqueries. In order to compensate for this (thus, to avoid classifying those pqueries as uncertain), we normalize the like_weight_ratios first, so that their sum is 1.0 again. This step thus ignores the uncertainties resulting from the placement algorithm.

  2. A path to a file, which needs to contain a single line for each taxon of the reference tree. Each line needs to contain a tab-separated entry that maps from a taxon of the tree to the clade name that this taxon belongs to:

    Taxon_1 <tab> clade_a
    

    (where the " <tab> " of course is just a single tab character). The taxa names need to be the same as the node names of the reference tree in the jplace file.

    If a taxon in a clade file is not found on the tree, a warning is issued, and the taxon is ignored. If the tree contains taxa which are not in any clade file, those branches are assigned to a special clade "basal_branches". This is also the case for the inner branches of the tree: all those branches which do not belong to one of the clades are collected in this special clade.

    As a second special clade, the "uncertain" clade is used to collect all those pqueries which did not fall into any clade with more than the threshold of accumulated likelihood weights.

    The edges that belong to a clade are determined by finding the smalles subtree (split) of the tree that contains all nodes of the clade. That means, the clades should be monophyletic in order for this algorithm to work properly. Furthermore, the user needs to make sure that each taxon is contained in at most one clade. Otherwise, the algorithm won't work properly.

    Remark: The rooting of the tree is insignificant for this program. Even if the root coincidentally lies within one of the clades, the result is the same. The program does not change the root; thus, when visualizing the clades, be aware that the tree might look different depending on the rooting.

  3. An output directory path. For each clade (including the two special clades), a jplace file named after the clade is written to that path. Each jplace file then contains all pqueries that were assigned to that clade.

A typical use case for this program is to extract pqueries that were placed in a particular clade of interest in an evolutionary placement analysis. The extracted placements can then be further examined in downstream analyses.

It is also possible to do a second run of evolutionary placement with the original sequences of the pqueries of one clade, using a refined reference tree for that clade with a higher resolution (more reference taxa). This two-step placement approach allows for finely grained placement positions while keeping the computational load relatively small.

Example

Example files to test the demo are located at

genesis/doc/demos/extract_clade_placements/

This directory contains an example.jplace file, a clades.tsv file listing the taxa of the reference tree of the jplace file and assigning each of them to either clade_a or clade_b, and an empty output directory.

After compiling the demo program (using make update), you can run the example like this

cd genesis/doc/demos/extract_clade_placements/
../../../bin/extract_clade_placements example.jplace clades.tsv output/

The expected output of the program is

INFO Using jplace file      example.jplace
INFO Using clade file       clades.tsv
INFO Using output directory output/
INFO Found 2 clades
INFO Finished.

You will then find four output files in ./doc/demos/extract_clade_placements/output/:

  • basal_branches.jplace contains 3 pqueries, which have most of their placement mass in the branches of the tree that do not belong to any of the two clades.
  • clade_a.jplace and clade_b.jplace contain 6 and 4 pqueries, which were located in those two clades.
  • uncertain.jplace contains a jplace file without any pqueries, as in this example all pqueries have more than the treshold of their mass in one clade (or in the basal branches).

Using this scaffolding, you can run the demo with your own data.