README-Examples.md

PolyMoSim examples:

PolyMoSim can be used in a variety of ways. Here we want to provide some examples how it can be used:

The following folders contain different examples. The purpose of these examples is mostly self explanatory.

Example-1_tree-in-Felsenstein-zone

Simulate a datasets on four taxon trees with a short internal branch such that methods like Maximum Parsimony are guaranteed to reconstruct the wrong phylogenetic tree.

Example-2_two-partitions

Simulate an alignment with two partitions.

Example-3_aa-models

Simulation using amino acid models.

Example-4_standard-heterotachy

Simulation producing an alignment with two partitions, simulating the standard heterotachy scenario.

Example-5_different-models-on-different-lineages

Simulations using different models on different lineages of the tree.

Example-6_free-siterate-distribution__remove_in_dist

Simulations using free rate models for the sequence evolution.

Example-7_heterotachy2__remove_in_dist

Example-for-sitepattern

Simulations that use site pattern frequencies as output format.