accuracy of gene tree simlation

[zzbbf123]

Hi Jeet,

i used follow command to simulate 1000 gene trees,and summarized gene tree clade frequencies for critical relationships by plotting them on the guide tree phylogeny with RAxML:

sp_tree is guide tree

num_rep=1000

genes_to_species_map = dendropy.TaxonNamespaceMapping.create_contained_taxon_mapping( containing_taxon_namespace=sp_tree.taxon_namespace num_contained=57 )

sp_tree = reconcile.ContainingTree(sp_tree, contained_taxon_namespace=genes_to_species_map.domain_taxon_namespace, contained_to_containing_taxon_map=genes_to_species_map)

sp_out = open("sp.txt", "w") for rep in range(num_rep): gene_tree1 = treesim.contained_coalescent_tree(containing_tree=sp_tree, gene_to_containing_taxon_map=genes_to_species_map) sp_out.write(gene_tree1.as_string(schema='newick'))

but the bootstrap value of each node so low (lower than 50%) that i can't help wondering what happens in my script or i just missing some very improtant message in your tutorials (https://dendropy.org/primer/treesims.html#simulating-contained-coalescent-trees).