Generating Species Trees

Basic Mode (T)

SimuLyon uses a Birth-death model to generate a species tree. Lineages can speciate given rise to two new lineages or go extinct over time.

Advanced Modes

Mode Tb - Branch-wise extinction and speciation rates

In this model, speciation and extinction rates are specific for each branch. Each time one new lineage emerges, a new value for its extinction and speciation rates its sampled from a user defined distribution (uniform, normal or lognormal). The difference with the previous model it is that rates are independently sample each time a new lineage emerge.

Mode Tp - Fine control of population

This model allows the user to fine control the size of the population

Mode Ta - Autocorrelation of extinction and speciation rates

In this model, speciation and extinction rates are specific for each branch. Each time one new lineage emerges, a new value for its extinction and speciation rates its sampled from a user defined distribution (normal or lognormal), in which the mean corresponds to the value of the parent branch and the variance to the branch length

Mode Ti - Preparing SimuLyon with an input tree by the user

This model allows the user to input a species tree

Output

WholeTree.nwk The whole species tree including the dead lineages, in newick format

ExtantTree.nwk The surviving species tree, in newick format

Events.tsv: Events (speciation and extinction) taking place in the species tree