DFOIL test (Pease & Hahn 2015)

DFOIL test for detecting and polarizing introgression in a 5-taxon symmetric phylogeny

Command identity

Canonical command:

dfoil

Handler:

dfoil

Aliases:

dfoil_test

Standalone executables:

pk_dfoil, pk_dfoil_test

Categories:

Introgression & gene flow

Runtime interface

Synopsis

phykit dfoil --alignment <alignment> --p1 <p1> --p2 <p2> --p3 <p3> --p4 <p4> --outgroup <outgroup> [--json]

Arguments

This table is generated from the live command parser. It is the authoritative source for accepted spellings, required arguments, types, defaults, and choices.

Argument	Required	Type	Default	Choices
-a, --alignment	true	str	required	any
--p1	true	str	required	any
--p2	true	str	required	any
--p3	true	str	required	any
--p4	true	str	required	any
--outgroup	true	str	required	any
--json	false	boolean	false	any

Output and errors

--json provides the command's structured JSON representation. Unless the guidance below states otherwise, results are emitted as command output. Invalid command syntax exits with status 2. Input validation and scientific limitations are described in the guidance below.

Guidance, interpretation, and examples

Compute DFOIL statistics (Pease & Hahn 2015) for detecting and polarizing introgression in a 5-taxon symmetric phylogeny with topology ((P1, P2), (P3, P4), Outgroup).

P1 and P2 are sister taxa; P3 and P4 are sister taxa; the two pairs are sister to each other, with an outgroup rooting the tree.

Four D-statistics are computed: DFO (far-outer), DIL (inner-left), DFI (far-inner), and DOL (outer-left). Each is tested for significance using a chi-squared test (1 df). The sign pattern of the four statistics maps to a specific introgression scenario via the lookup table from Pease & Hahn (2015).

phykit dfoil -a <alignment> --p1 <taxon> --p2 <taxon> --p3 <taxon> \
    --p4 <taxon> --outgroup <taxon> [--json]

Options:
-a/--alignment: FASTA alignment file (required)
--p1: taxon name for P1, sister to P2 (required)
--p2: taxon name for P2, sister to P1 (required)
--p3: taxon name for P3, sister to P4 (required)
--p4: taxon name for P4, sister to P3 (required)
--outgroup: outgroup taxon name (required)
--json: optional argument to print results as JSON