99% of the time, all you want is: 2015-03-16: I have done a pretty massive update to the BEASTmaste R code (see "Files" at the bottom of this page), fixing some bugs, improving error checking (although it's impossible to think of everything), and adding many new features that I, at least, find interesting.Writing an XML file that will actually function in Beast2 is a complex task. Even doing it with BEAUTI, despite many useful BEAUTI features, can cause numerous headaches.These periods are hypothesized to have led to fragmentation and isolation of feeding regions leading to possible regional extinctions, as well as the promotion of allopatric speciation.The closely shared evolutionary history of mobulids in combination with ongoing threats from fisheries and climate change effects on upwelling and food supply, reinforces the case for greater protection of this charismatic family of pelagic filter feeders.The order Piroplasmida consists of several genera of tick-borne parasites that infect mammals, and to a lesser extent birds, and are therefore of medical and economic importance.Despite their importance, considerable confusion exists concerning the relationship among piroplasmid species, specifically concerning the number of genera and the intergeneric relationships.
Finally, we call for a comprehensive phylogenetic, morphological and life-history analysis for these medically relevant taxa to resolve relationships and understand host specificity.► Piroplasmids are pathogenic hemoparasites infecting an array of mammalian hosts.(These include, e.g., not saving your setup; manually entering clades, dates, etc; bewildering variety of options; lack of features needed for fossil tip-dating; and occasional bugs. It is just a very difficult task to write a general-purpose XML writer that will cover everything a user might want, and do so in the face of continuing evolution of needs, Beast code base, packages, etc.).Writing a generic R program to do EVERYTHING would also be very diffcult.Manta and devil rays are an iconic group of globally distributed pelagic filter feeders, yet their evolutionary history remains enigmatic.We employed next generation sequencing of mitogenomes for nine of the 11 recognized species and two outgroups; as well as additional Sanger sequencing of two mitochondrial and two nuclear genes in an extended taxon sampling set.The purpose of "BEASTmaste R" is to convert NEXUS data file(s) (DNA, amino acids, discrete morphological characters, and/or continuous traits), plus an Excel settings file, into Beast2 XML format. The Birth-Death-Skyline-Serial-Sampling tree model is used (or the Sampled-Ancestors variant), enabling different birth, death, and sampling rates through time. Of course, identified bugs I will always try to fix or post work-arounds. BEASTmaste R is primarily aimed at enabling tip-dating analyses using fossils as dated terminal taxa. If you want any serious help/feature additions with BEASTmaste R, for me, given my current commitments, that feels more like a coauthorship-type situation than a generic-free-help situation. Ideally, there will be a release with a DOI, but it may be you just use the most up-to-date commit. pre-release 0.1 is at https://github.com/nmatzke/BEASTmaste R/releases/tag/0.1 , and has DOI . I am happy for BEASTmaste R to be a resource for the phylogenetics community, however. , used for extracting the bracketed statistics from BEAST NEXUS tree files (MCC files) are copied/lightly modified/heavily modified from the R package " phyloch", by Christoph Heibl, licensed under GPL ( BEASTmaste R was originally aimed at easing my own tip-dating work in Beast2, and at the participants of the Tip-Dating Workshop and Putting Fossils in Trees Symposium at the 2014 meeting of the Society for Vertebrate Paleontology, in Berlin.BEASTmaste R will eventually become an R package and have a publication associated with it. 2015-10-08: The BEASTmaste R code has been moved to Git Hub (https://github.com/nmatzke/BEASTmaste R ). I will continue to maintain instructions & updates at Phylo Wiki. Of course, I cannot promise that I can give everyone outside a workshop detailed help — producing an R package, documentation, and a publication about BEASTmaste R would have priority, as would help about my main package, Bio Geo BEARS.