phylotypes 2.0.1

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.

--distance {legacy,kr} Pairwise distance metric. legacy (default) is an exact, vectorized reimplementation of the original LCA-weighted-average metric and reproduces prior phylotypes. kr is the true tree-Wasserstein (Kantorovich-Rubinstein) distance, a proper metric -- opt-in.

Note: --threshold_pd's default of 1.0 is calibrated for --distance legacy. The kr metric is on a different (smaller-valued) scale, so the same threshold means a different cut. If you use --distance kr, re-calibrate --threshold_pd on your own data; the legacy default will over- or under-split. (No default kr threshold is provided yet -- this is a TODO pending empirical calibration on a real dataset.)

--no-distal-length Ignore distal length to nodes when computing distances. Default is False (distal length is included).

--incremental Use an incremental seed→apply→expand→reconcile clustering path instead of the default batch path. Scales to larger inputs with lower peak memory at the cost of approximate (single/centroid-like) linkage near phylotype boundaries.

--seed-size <int> Number of (most specific) placements used to seed the initial phylotype pool when --incremental is set. Default: 200.

--expand-batch-size <int> Maximum number of orphaned placements clustered together per expand pass when --incremental is set. Default: 200.

--device <str> PyTorch device for tensor computations, e.g. cpu or cuda. Default: cpu.

--max-pregroup-size <int> Maximum SVs in a single pregroup after LCA-based re-clustering; larger pregroups are split back to their pre-merge groups to bound memory use. Default: 5000.

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add_phylotypes

Assign a new set of placed sequence variants into an existing set of phylotypes.

Given a previous JPLACE file and its phylotype assignments (produced by phylotypes), and a new JPLACE of sequence variants placed on the same reference tree, each new SV is assigned to the nearest existing phylotype.

Input:

--previous_jp / -P <file> Previous JPLACE file (same reference tree as --new_jp).

--previous_phylotypes / -p <file> CSV file with two columns (phylotype, sv) representing the existing phylotype assignments.

--new_jp / -N <file> New JPLACE file containing the sequence variants to be assigned.

Output:

--out / -O <file> Output CSV (phylotype, sv) placing the new SVs into the existing phylotypes. SVs that share no tree-edge overlap with any existing phylotype are reported as orphans in the log and omitted from the output.

Parameters:

--no-distal-length Ignore distal length when computing distances. Default: False.

--device <str> PyTorch device. Default: cpu.

--distance {legacy,kr} Pairwise distance metric. Default: legacy.

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phylotype_taxonomy

Assign a consensus species (or best-effort taxon) to each phylotype using per-SV taxonomic annotations.

Input:

--phylotypes / -p <file> CSV with phylotype and sv columns (output of phylotypes).

--taxonomy / -t <file> Per-SV taxonomic assignments in long format (as produced by MaLiAmPi), with columns sv, rank, want_rank, and tax_name.

Output:

--out / -O <file> CSV with phylotype and species columns. Phylotypes without a species-level assignment are annotated at the best available rank with a spp. suffix.

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Release notes

v2.0.1

• add_phylotypes now shares the same JPLACE loader and distance metric as phylotypes, eliminating a divergent implementation that failed on standard SEPP/epa-ng edge-numbered trees.
• New --incremental clustering path for large datasets.
• GPU support via --device cuda (or any valid PyTorch device string).
• KR-distance threshold caveat: the --distance kr metric is on a different (smaller-valued) scale than legacy. The default --threshold_pd 1.0 is calibrated for legacy only. If using --distance kr, re-calibrate the threshold on your own data.