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Advanced Search Abstract Motivation: Phylogenies are increasingly used in all fields of medical and biological research.

Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML Randomized Axelerated Maximum Likelihood is a popular program for phylogenetic analyses of large datasets under maximum likelihood.

Since the last RAxML paper init has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community.

I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees.

In addition, an up-to-date page user manual covering all new RAxML options is available. Supplementary data are available at Bioinformatics online. Its major strength is a fast maximum likelihood tree search algorithm that returns trees with good likelihood scores.

Since the last RAxML paper Stamatakis,it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community.

It implements the standard non-parametric bootstrap and also the so-called rapid bootstrap Stamatakis et al. It also offers an option to calculate the so-called SH-like support values Guindon et al. When this option is used, RAxML will automatically determine how many bootstrap replicates are required to obtain stable support values.

It can correct for ascertainment bias Lewis, for all of the above data types. This might be useful not only for morphological data matrices that only contain variable sites but also for alignments of SNPs.

The number of available protein substitution models has been significantly extended and comprises a general time reversible GTR model, as well as the computationally more complex LG4M and LG4X models Le et al.

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RAxML can also automatically determine the best-scoring protein substitution model. Finally, a new option for conducting a maximum likelihood estimate of the base frequencies has become available. Note that, for extremely large analyses on supercomputers, using the dedicated sister program ExaML [Exascale Maximum Likelihood Stamatakis and Aberer, ] is recommended.

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Apart from standard statistical significance tests, it offers efficient and partially parallelized operations for computing Robinson—Foulds distances, as well as extended majority rule, majority rule and strict consensus trees Aberer et al.

Beyond this, it implements a method for identifying the so-called rogue taxa Pattengale et al. Finally, there is the new plausibility checker option Dao et al. This option can be used to automatically assess the quality of huge trees that can not be inspected by eye. A sliding-window approach unpublished is available to assess which regions of a gene e.

It also offers placement support statistics for those reads by calculating likelihood weights. This option can also be used to place fossils into a given phylogeny Berger and Stamatakis, or to insert different outgroups into the tree a posteriori, that is, after the inference of the ingroup phylogeny.

The memory savings are proportional to the amount of missing data in the alignment Izquierdo-Carrasco et al.Download MDSolids (Microsoft MSI Installer Version) (8/15/, 18 MB) The registration code is D93C8ADC. In honor of Dr. Philpot's tireless dedication to engineering education, the Philpot family is offering free access to the full version of MDSolids.

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