ANGST

the ANalyzer of Gene and Species Trees.
by Lawrence David and Eric Alm
ANGST
UPDATE
Run AnGST online using the AnGST online server. Simply upload your tree files and processing takes place on our servers. Does not require code downloading or prior programming knowledge!

Several algorithmic approaches for the inference of prokaryotic gene family evolutionary histories have been proposed. Although divergent in their backgrounds, these algorithms are united by a common goal: the proposal of a series of horizontal gene transfer (HGT), gene duplication (DUP) and gene loss (LOS) events to explain observed distributions of orthologous genes amongst extant prokaryotic genomes. Regrettably, these inference algorithms also all share at least one of the following shortcomings: 1) an inability to model both HGT and DUP simultaneously; 2) an inability to incorporate ortholog phylogenetic information; 3) a lack of robustness to phylogenetic construction errors. We avoid all three of these limitations in a novel algorithm that we have developed, entitled the Analyzer of Gene and Species Trees (AnGST). In brief, AnGST performs a phylogenetic reconciliation between a given species and gene tree, positing the best scoring set of HGT, DUP, and LOS events to explain all topological incongruities between the two trees. In order to protect against phylogenetic noise, we have designed AnGST to be capable of incorporating information from dozens of bootstrap trees simultaneously. In cases of variations among bootstrap subtrees, the subtree that best accords with the reference tree is adopted.

References
(1) Lawrence A. David and Eric J. Alm. “Rapid evolutionary innovation during an Archean Genetic Expansion.” Nature, Vol. 469, No. 7328. (6 January 2011), pp. 93-96.

Source code
github