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
