Deleterious changes between 0.3.5c and 0.3.6

[BenoitMorel]

Hello,

I ran Deleterious on simulated datasets, with both versions 0.3.5c and 0.3.6.
I observed that 0.3.5c is much slower but also finds much better (in terms of RF distance to the true gene trees) trees than 0.3.6 and 0.3.7.

Is this expected? Are there any big difference between both versions?

Here is one example command line I use:
java -Xms512m -Xmx1024m -jar prime_0.3.5c.jar Deleterious speciesTree.newick alignment.msa mapping.link -i 10000 -t 10 -s 42 --siteratecategories 4 -sm JC69 -o output

Adding more iterations does not fix the issue. I pick the resulting gene tree from the info file to compute the RF distance to the true tree.

Best,
Benoit