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.
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