Enveomics collection

Newick.autoprune.R

Automatically prunes a tree, to keep representatives of each clade.

    See source code, Artistic license 2.0.

§ References

    Paradis et al, 2004, Bioinf; Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

• R.
• R package optparse.
• R package ape.

§ Usage

Newick.autoprune.R --t in_file [opts] out_file

§ Arguments

Input tree*

 --t in_file  A tree to prune in Newick format.

Dist quantile

 --dist-quantile float  The quantile of edge lengths.

Min dist

 --min_dist float  The minimum distance to allow between two tips. If not set, dist.quantile is used instead to calculate it.

Quiet

 --quiet   Boolean indicating if the function must run without output.

Max iters

 --max_iters integer  Maximum number of iterations.

Min nodes random

 --min_nodes_random integer  Minimum number of nodes to trigger 'tip-pairs' nodes sampling. This sampling is less reproducible and more computationally expensive, but it's the only solution if the cophenetic matrix exceeds 2^31-1 entries; above that, it cannot be represented in R.

Random nodes frx

 --random_nodes_frx float  Fraction of the nodes to be sampled if more than 'Min nodes random'.

Output file*

 out_file  Output file in Newick format containing the pruned tree.

* Mandatory.