TreeAnnotator.MemoryFriendlyTreeSet is used in quite a few BEAST apps for post-processing trees, and is supposed to deal with both NEXUS files containing trees and Newick tree sets. However, it fails to determine the taxa in a Newick tree set. Since it is easier to produce Newick tree files for BEAST apps that produce tree sets in their output (e.g. TaxonFilter in the Babel package) this means a translation is required from Newick to NEXUS (e.g. using the Newick2Nexus app in Babel) for subsequent post-processing.
Fixing the TreeAnnotator.MemoryFriendlyTreeSet so it can deal with Newick tree sets would mean that this step is no longer required.
TreeAnnotator.MemoryFriendlyTreeSet is used in quite a few BEAST apps for post-processing trees, and is supposed to deal with both NEXUS files containing trees and Newick tree sets. However, it fails to determine the taxa in a Newick tree set. Since it is easier to produce Newick tree files for BEAST apps that produce tree sets in their output (e.g. TaxonFilter in the Babel package) this means a translation is required from Newick to NEXUS (e.g. using the Newick2Nexus app in Babel) for subsequent post-processing.
Fixing the TreeAnnotator.MemoryFriendlyTreeSet so it can deal with Newick tree sets would mean that this step is no longer required.