ASAP – Assemble Species by Automatic Partitions

Delimits species from aligned sequences using the algorithm of Puillandre, Brouillet & Achaz (2021). The original C code (asap_core.c, asap_common.c) is executed without modifications; only the Python/graphical dependencies are replaced.

Usage

asap(
  x,
  model = "simple",
  len_seq = NULL,
  replicates = 1000L,
  pvalue_threshold = 0.001,
  slope_weight = 0.1,
  score_weight = 0.5,
  pairwise.deletion = TRUE
)

Arguments

x

Path to an aligned FASTA file, or an aligned DNAbin (ape) object. Distance matrices are not accepted; distances are calculated internally from the sequences.

model

Distance model. "simple" (default) uses Simple_Dist, identical to the ASAP original default. Any model from ape::dist.dna() is also accepted.

len_seq

Sequence length for the coalescent simulations. Inferred from the alignment length when NULL (default).

replicates

Coalescent replicates. Default: 1000.

pvalue_threshold

P-value threshold. Default: 0.001.

slope_weight

Slope window weight. Default: 0.1.

score_weight

Weight of the p-value rank in the ASAP-score. Default: 0.5.

pairwise.deletion

Passed to ape::dist.dna(). Default: TRUE.

Value

A list of class "asap" with:

partitions

data.frame sorted by ascending ASAP-score.

best

List with the best partition (rank 1).

dist_matrix

Distance matrix used.

taxa

Sequence names.

AI Disclaimer

This function was written with assistance of AI coding agent (Claude Code Sonnet 4.6). Correctness was validated by comparing against original software, on a suite of real sequencing datasets, and manual code review. All validation and output

Source Code

N. Puillandre, A. Lambert, S. Brouillet, G. Achaz (ASAP C engine)

References

Puillandre N, Brouillet S, Achaz G (2021). ASAP: assemble species by automatic partitions. Molecular Ecology Resources, 21(2), 609-620. doi:10.1111/1755-0998.13281

Author

Pedro S. Bittencourt

Examples

if (FALSE) { # \dontrun{
library(ape)
seqs   <- read.dna("barcode.fasta", format = "fasta")
result <- asap(seqs)
result <- asap("barcode.fasta")   # aligned FASTA path also accepted
print(result)
bp <- best_partition(result)
bp$n_groups   # number of species
bp$partition  # assignment for each sequence
} # }