Phylogenetic_Validation

Analyse PAFTOL tree and label nodes

Method

The program has two main tasks: First: to identify the nodes corresponding to higher taxa, such as family or order; Second: to confirm or reject samples at these taxonomic ranks, based on their placement within or outside these nodes, respectively.

1. For every node in the tree, two metrics were calculated: (i) the proportion of samples belonging to a taxon (e.g. family) that subtended the node, and (ii) the proportion of samples subtending the node that belonged to that taxon. The two metrics were then multiplied to produce a combined score. For each taxon, the highest scoring node was subsequently considered to best represent the taxon in the tree. Each node corresponding to a taxon were categorized as (i) well-resolved when reaching a score of 1, (ii) resolved when <1 but >0.5, (iii) poorly resolved if the score was <0.5.

2. The phylogenetic validation of family identification of each sample was determined as:

   a. Confirmed: if identified as belonging to a family whose best scoring node had a value >0.5 and found as a descendant of this node in the tree.

   b. Rejected: if identified as belonging to a family whose best scoring node had a value >0.5 but not found as a descendant of this node.

   c. Inconclusive: if belonging to a family whose best scoring node had a value ≤0.5.

Note that for families represented in the tree by a single sample, the validation was performed with respect to their orders. If the order was represented by a single sample, the sample was considered untestable and coded as inconclusive.

Usage

Inputs:

• opt_tree Input tree (required)
• opt_dup is an (optional) list of PAFTOL entries to disregard
• opt_root is the node ID of the true root. Need to find this manually based on content of tree

perl pp.pl -tree treefile.nwk [-dup.dup.txt] -good g.txt -alien a.txt -outlier o.txt -specimen s.txt -tree2 new_treefile.nwk [-root 100000] [-order] [-well] [-help] > output.txt

Options:

• tree=s Input (unrooted) tree in Newick format
• dup=s Optional list of nodes to ignore
• good=s List of all specimens not needed for manual review (if running on a pre-tree)
• bad=s List of badly resolving higher taxa
• alien=s List of all specimens intruding in well-defined families
• outlier=s List of all taxa outlying an ancestral taxon
• specimen=s List of score for how well each specimen matches to its family
• tree2=s File to which a simplified (rooted) family-level tree will be written
• root=i Node to be used to root the new tree
• order Specify this to write a simplified order-level tree instead of a family level tree
• well Specify this and specimens will only be considered outliers to well-defined parents
• help Prints out usage

Outputs:

The program produces:

• A list of outliers (i.e. samples not found under the node best describing their family) and aliens (i.e. samples found in a resolved family but not belonging to it). Note that by default the program produces a summary of the tree for families, but it can used for other taxonomic levels (e.g. order, genus)
• Taxonomic clashes (inconsistent families and orders)
• The proportion of monophyletic nodes at each level of the taxonomy
• The proportion of monophyletic nodes at each level of the taxonomy
• mean %consistency of each taxonomic head node at each maximum taxonomic group size
• family match score for each species
• summary, rooted species and family level trees