phylotypes 1.0.0

Group phylogenetically placed sequence variants into phylotypes

Phylotypes

Group features (e.g. 16s rRNA gene variable region sequence variants) placed on a common phylogenetic tree by phylogenetic distance.

This is particularly useful when attempting a metanalysis of 16s rRNA gene variable region amplicons, in which the amplicons were made with different primers, etc.

Input:

--jplace <file> A jplace file (deduplicated) as made by pplacer or epa-ng.

Output:

--out <file> Path where the output should be placed in CSV format. This will be a header-containing CSV file in long-format with two columns: phylogroup and feature-id.

Parameters:

--lwr-overlap <0.0 - 1.0> Minimum like-weight-ratio overlap for two placed features (e.g. sequence variants) to be pre-grouped. Default of 0.1 should be fine for most use cases.

--threshold_pd <float> Phylogenetic distance at which to cluster features. Default of 1.0 corresponds roughly to somewhere between species-level and genus-level grouping for 16s rRNA V4 region amplicons.