Usage

This section covers practical OrthoSNAP usage. For a full worked example, see the tutorial.

OrthoSNAP takes:

• a gene tree in Newick format

• the FASTA file used to infer that tree

It outputs one FASTA file per inferred SNAP-OG (single-copy orthologous subgroup). Optionally, it can also write a Newick tree per SNAP-OG, an inparalog handling report, and one color-coded subgroup plot for the full input tree.

Basic usage

For most cases, only -f/–fasta and -t/–tree are required:

$ orthosnap -f orthogroup_of_genes.faa -t phylogeny_of_orthogroup_of_genes.tre

Input requirements

• FASTA headers and tree tip labels must match.

• Taxon and sequence IDs must be separated by the same delimiter in both files.

• Default delimiter is | (for example, species_A|gene_001).

Accounting for tree uncertainty

OrthoSNAP can collapse low-support bipartitions before pruning inparalogs.

• Default support threshold is 80.

• Use -s/–support to change it.

$ orthosnap -f orthogroup_of_genes.faa -t phylogeny_of_orthogroup_of_genes.tre -s 70

Choosing which inparalog to keep

Use -ip/–inparalog_to_keep to select how species-specific inparalogs are resolved.

Supported values:

• shortest_seq_len

• median_seq_len

• longest_seq_len (default)

• shortest_branch_len

• median_branch_len

• longest_branch_len

Examples:

$ orthosnap -f orthogroup_of_genes.faa -t phylogeny_of_orthogroup_of_genes.tre -ip shortest_branch_len

$ orthosnap -f orthogroup_of_genes.faa -t phylogeny_of_orthogroup_of_genes.tre -ip median_seq_len

Inparalog handling report

Use -rih/–report_inparalog_handling to write a tab-delimited report named <input_fasta>.inparalog_report.txt.

Columns are:

• SNAP-OG identifier

• kept inparalog

• trimmed inparalog(s), separated by ;

$ orthosnap -f orthogroup_of_genes.faa -t phylogeny_of_orthogroup_of_genes.tre -rih

Specifying the delimiter

If your headers do not use |, specify the delimiter with -d/–delimiter.

$ orthosnap -f orthogroup_of_genes.faa -t phylogeny_of_orthogroup_of_genes.tre -d -

Plotting SNAP-OG assignments

Use -ps/–plot_snap_ogs to create one figure of the full tree with distinct colors for each inferred SNAP-OG. Default plot format is PNG; choose PDF or SVG with -pf/–plot_format.

$ orthosnap -f orthogroup_of_genes.faa -t phylogeny_of_orthogroup_of_genes.tre -ps

$ orthosnap -f orthogroup_of_genes.faa -t phylogeny_of_orthogroup_of_genes.tre -ps -pf svg

Example output (png):

Performance Benchmark

The chart below summarizes benchmarked runtime across selected PyPI releases and the current local version. Runs used a rooted input tree (-r), one warm-up run per version, and three measured runs per version on the same dataset.

Compared versions:

• 1.1.0 (PyPI baseline)

• 1.2.0 (PyPI)

• 1.3.2 (PyPI)

• 1.5.0-current (local)

All options

Option	Meaning
-h/--help	Print help message.
-v/--version	Print software version.
-f/--fasta	Input FASTA file.
-t/--tree	Input tree file in Newick format.
-s/--support	Collapse threshold for branch support (default: 80).
-o/--occupancy	Minimum represented taxa for subgroup candidates (default: rounded half of taxa in input FASTA).
-r/--rooted	Treat input tree as rooted; otherwise midpoint-root it (default: false).
-d/--delimiter	Delimiter between taxon and sequence IDs (default: |).
-st/--snap_trees	Also write SNAP-OG trees in Newick format (default: false).
-ip/--inparalog_to_keep	Rule for keeping one inparalog among species-specific duplicates (default: longest_seq_len).
-rih/--report_inparalog_handling	Write tab-delimited inparalog handling report (default: false).
-op/--output_path	Output directory (default: directory containing input FASTA).
-ps/--plot_snap_ogs	Write one color-coded full-tree plot with subgroup labels (default: false).
-pf/--plot_format	Output format for subgroup plot (png default, or pdf/svg).

For genome-scale analyses, consider using the same -o/–occupancy value across all gene families to keep SNAP-OG occupancy thresholds consistent.