Outgroup rooting -outgroup o1,o2.,oN option specifies outgroups when drawing a tree Conversely, if some taxa are missing from the constraint, they will be placed freely in the resulting ML tree. If the constraint tree is comprehensive (i.e., it includes all taxa found in the MSA), then RAxML will simply resolve polytomies in the way that maximizes the likelihood. Topological constraint -constraint-tree FILE option specifies a constraint tree This approach is a compromise that allows to model distinct evolutionary rates across partitions while introducing only a moderate number of free parameters ( #branches + #partitions). scaled ( proportional): a global set of branch lengths is estimated like in linked mode, but each partition has an individual scaling factor per-partition branch lengths are obtained by multiplying the global branch lengths with these individual scalers.This model allows for the highest flexibility, but it also introduces a huge number of free parameters ( #branches * #partitions), which makes it prone to overfitting. unlinked: each partition has its own, independent set of branch lengths.However, it is often considered too unrealistic, since it is known that genes (or genome regions) evolve at different speeds. This is the simplest model with fewest parameters ( #branches). linked: all partitions share a common set of (global) branch lengths.In partitioned analyses, there are three common ways to estimate branch lengths (sometimes called branch linkage modes): GTR+G+FO, COXp1_2=1249-4482/3,1250-4482/3īeware of branch lengths -brlen option sets the branch linkage model If the problems are found, a “cleaned” file Sites with only undetermined characters or sequences with undetermined characters check command checks that the MSA can actually be read and doesn’t contain Checking/optimizing your data Use the -check command to check/optimize your dataset. RAxML-NG will generate several output files. Output -prefix option (optional) addes prefix to output files. model option (required) specifies the model of evolution.Įxamples of possible models are GTR+G for nucleotide data, JTT+G for aa data,īIN for binary data, MULTI8_MK multistate data with 8 categories, among You can also specify the alignment format explicitly with the RAxML-NG supports alignments in FASTA, PHYLIP and CATG formats.īy default, RAxML-NG will try to automatically detect alignment format based on
msa option (required) specifies alignment So we have to specify our data and our model in all raxml-ng commands. Remember that likelihood is the probability of the data given the model (P(D|M)). More comprehensive documentation is available in GitHub wiki. Getting help -help option displays the help menu (you can also run raxml-ng without parameters).