Autumn algorithm - supplementary data

This page provides supplementary data for the following paper: Huson, D.H. and S. Linz, Autumn Algorithm - Computation of Hybridization Networks on Realistic Phylogenetic Trees, presented at APBC 2016, to appear in Trends in Computational Biology and Bioinformatics.

Figures 4 and 5:

Cichlids.nexml
Cichlids-hybridization-networks.nexml

Reference: S. Koblmueller, N. Duftner, K. Sefc, M. Aibara, M. Stipacek, M. Blanc, B. Egger, and C. Sturmbauer, Reticulate phylogeny of gastropod-shell-breeding cichlids from lake tanganyika - the result of repeated introgressive hybridization, BMC Evolutionary Biology, vol. 7, no. 1, p. 7, 2007. Link.

Table 1:

ndhF-phyB-original.nexml
ndhF-rbcL-original.nexml
ndhF-rpoC2-original.nexml
ndhF-GBSS-original.nexml
ndhF-ITS-original.nexml
phyB-rbcL-original.nexml
phyB-rpoC2-original.nexml
phyB-GBSS-original.nexml
phyB-ITS-original.nexml
rbcL-rpoC2-original.nexml
rbcL-GSSB-original.nexml
rbcL-ITS-original.nexml
rpoC2-GBSS-original.nexml
rpoC2-ITS-original.nexml
GBSS-ITS-original.nexml

Reference: Grass Phylogeny Working Group, Phylogeny and subfamilial classification of the grasses (Poaceae), Annals of the Missouri Botanical Garden, vol. 88, no. 3, pp. 373-457, 2001.

Other grasses example:

Danthonioideaea-Chloroplast+ITS.nexml

Reference: M. D. Pirie, A. M. Humphreys, N. P. Barker, and H. P. Linder, Reticulation, data combination, and inferring evolutionary history: an example from Danthonioideae (Poaceae), Syst Biol, vol. 58, no. 6, pp. 612-28, 2009.

Nymphoides example:

Nymphoides.nexml

Reference: N. P. Tippery and D. H. Les, Phylogenetic relationships and morphological evolution in nymphoides (menyanthaceae), Systematic Botany, vol. 36, no. 4, pp. 1101-1113, 2011.

Implementation:

The autumn algorithm is implemented in Dendroscope (menu item Algorithms-Hybridization Networks...). This program is freely available here: Dendroscope