ALE_analysis

Calculating transfers to and from each branch on the species tree

In examing gene family transfers it may be of interest to examine lateral gene transfer donors, as well as recipients. The calc_from_to_T.sh script manipulates results from the ALE output transfer frequency files (ending .uTs) to identify branches of species trees with high numbers of gene family donation, as well as receipt.

Sample data for testing workflows

To test that things are working as expected, it may be convenient to experiment with the files in Example100_uTs.tar.gz in this repository.

Usage

Run script in directory containing the transfer frequency files (ending .uTs) from the ALE gene tree-species tree reconciliations.

sh calc_from_to_T.sh

Output file: From_to_T.txt

Example output

Branch	From	To
100	1.26	2.66
101	2.41	3.46
102	6.94	10.29
103	6.68	9.72
104	1.5	6.56