abgd web

For now Jukes-Cantor distances and Kimura 2-P are available, but Tamura-Nei will be added very soon (please use an input distance matrix in the mean-time)

The method scans a range of Prior Intraspecific divergence from Pmin to Pmax, with P Steps. The X value is a proxy for the minimum relative gap width. For more details, please refer to the ABGD manuscript.

Choose an input file
It can either be an already ALIGNED fasta file or a distance matrix (format from phylip dnadist or MEGA)

IMPORTANT:If you have a distance MEGA distance file please select format: MEGA MEGA CSV


Or paste your data (FASTA alignement) here

if you select a file AND paste data, only the pasted data will be processed

Pmin   Pmax   Steps

X (relative gap width):

Nb bins (for distance distribution) :

If you enter a fasta file you can select your distance: Jukes-Cantor(JC69) Kimura (K80) TS/TV Simple Distance


Browsers that have been successfully tested include: FireFox and Safari. Please report any problems to sophie.brouillet@mnhn.fr

If you have less than 700 sequences, for each partition, a newick tree will be build using BIONJ software and a rough visualisation will be done by newick_utils.
With more than 700 sequences, if you need to build a tree, you have to download the online version and run abgd in command line mode

See "BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data." Gascuel O. Molecular Biology and Evolution. 1997 14:685-695. for more about BIONJ See "The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell" Junier T. and Zdobnov E. M. Bioinformatics (2010) 26(13): 1669-1670"for more about newick_utils


s