In-paralogous

Instances implementing the interface Inparalogous are used to removing in-paralogous. If you want to define your own in-paralog-handler, extend AbstractInparalogous and the abstract tag found in the def.xml file. For more information see section Create a Tag Instance.

InparalogousStandard is the standard procedure to remove in-paralogous in Softparsmap and its tag did="standard" has following attributes.

• remove_before_saving - determines if in-paralogous are removed before saving the final tree or not. The attribute can only be yes or no.

• remove_while_minimizing_mutation - determines if in-paralogous are removed while minimizing mutation. The attribute can only be yes or no. The method finds the list by rooting the free gene tree at one edge at the time and then inferring mutation. Before inferring mutation it is possible to remove in-paralogous.

In order to choose the right sequence to replace the rooted subtree, the algorithm is first sorting the sequences using a compare sorting algorithm and then as the last step, the first in the sorted result is chosen. The procedure used to compare two sequences A and B is as follows.

1. if A is complete and B is not, A is preferred,

2. if the item above could not decide then if B is complete and A is not, B is preferred

3. if items above could not decide then if A is longer then B then A is preferred

4. if items above could not decide then if B is longer then A then B is preferred

5. if items above could not decide then if A's GI number is higher then B's GI number, then A is preferred

6. if items above could not decide then if B's GI number is higher then A's GI number, then B is preferred

7. if items above could not decide then A is preferred. It has to choose one