ABGD

Introduction ABGD

The Automatic Barcode Gap Discovery (ABGD, Puillandre et al., 2012) is a delimitation method based on genetic distances of single barconding genes. The main assumption of the method is that the divergence among organisms of the same species is smaller than the divergence among organisms of different species. This is the well-known "barcode gap" assumption which was initially introduced by Hebert et al., 2003.

The method performs the following steps in an attempt to automatically identify the barcoding gap:

1. Sorts the pairwise distances of the aligned sequences (there is the option for using substitution models for corrected distances).

2. Based on a prior belief on the intraspecific divergence (Pmin - Pmax) and a proxy (X) for the minimum width of the gap, the method identifies the largest gap and assumes it is corresponds to barcoding gap.

3. After identifying the barcoding gap, it divides the sequences into candidate species and repeats the above steps (1-2) to each of them.

Software:

ABGD is available as a website and as a standalone software implemented in C.

Input: Aligned fasta file or distance matrix

Install:

$ wget http://wwwabi.snv.jussieu.fr/public/abgd/last.tgz

$ tar -xvzf last.tgz

$ cd Abgd 

$ make

Exercise

Infer alignment:

$ mafft BR_cob_57ind_no_out.fasta > BR_cob_57ind_no_out_mafft.fasta

BR_cob_57ind_no_out.fasta

BR_cob_57ind_no_out_mafft.fasta

ABGD delimitation with some known distance threshold

$ abgd -p 0.03 -P 0.03 -n 1 BR_cob_57ind_no_out_mafft.fasta
Partition 1 : 10 / 10 groups with / out recursion for P= 0.030000
---------------------------------
Results file are :
Graphic svg file sumarizing this abgd run: ./BR_cob_57ind_no_out_mafft.abgd.svg
Graphic distance histogram svg file : ./BR_cob_57ind_no_out_mafft.disthist.svg
Graphic rank distance svg file : ./BR_cob_57ind_no_out_mafft.rank.svg
---------------------------------

ABGD delimitation with a range of distance thresholds

$ abgd -p 0.001 -P 0.03 BR_cob_57ind_no_out_mafft.fasta

output files:

BR_cob_57ind_no_out_mafft.abgd.svg

BR_cob_57ind_no_out_mafft.disthist.svg

BR_cob_57ind_no_out_mafft.rank.svg

ABGD delimitation with a range of distance thresholds and proxies for the gap width (optional)

$ abgd -p 0.001 -P 0.1 BR_cob_57ind_no_out_mafft.fasta -X 1

$ abgd -p 0.001 -P 0.1 BR_cob_57ind_no_out_mafft.fasta -X 2

$ abgd -p 0.001 -P 0.1 BR_cob_57ind_no_out_mafft.fasta -X 3

Repeat the exercise for the Carabus alignment

Download the output files here