Diego Mallo

This bug relates to the bounded-subtree output file (-ON option, see https://github.com/adamallo/SimPhy/wiki/Manual#532-bounded-locus-subtrees-output-file-format) but does not affect the more commonly used mapping files. This problem should be solved in SimPhy's development...

Just for clarification, the old version should still allow you to map species and locus trees. However, that format is quite complicated, and a lot of people are having problems...

> Hi, > > It seems that, after setting the OL parameter to 1, the internal nodes of the species tree in s_tree.trees file are numbered in inorder, while the...

> Hi, It's been a long time, but I am facing the same issue. Below are a species tree (left) and a locus tree (right) with the nodes as labeled...

Hi Alexandra, After a quick look at the error SimPhy is returning, it seems to me that the problem may be in the text encoding. SimPhy is expecting plain ASCII,...