7.6.2. Using SATé
An alternative software package to MEGA for ML analyses is SATé (Simultaneous Alignment and Tree estimation; Liu et al., 2012), which infers sequence alignment and tree building concurrently as an iterative process using the ML method. This program must also be downloaded for use, and is currently freely available as SATé-II at http://phylo.bio.ku.edu/software/state/sate.html. The user experience for SATé is still being improved, including recommendations for how to parse phylogenetic runs. A strength of SATé is that it accepts up to 1,000 sequences in the fasta format as described in section 7.3., and claims speed and precision in phylogenetic analyses. Through changes in subproblem size parameters (below) it is possible to run SATé on desktop machines, but using this software on high-memory and high-CPU clusters will be simpler since those parameters will be less likely to affect performance. Several alignment programs are bundled with the download, including Clustal and MUSCLE. If an alignment is already prepared, SATé will use Randomized a(x)- elerated Maximum Likelihood (RaxML) (Satmatakis, 2006) to infer an initial tree for phylogeny reconstruction.
the main SATé window, select the desired analysis criteria in the following