sate-dev/sate-core — Issue #5: Sequences appear twice in the Alignment output file
Author: smirarab
Created: 2011-11-02 22:13:07+00:00
State: open

For some reason sequences appear twice in my output alignment, one time with the correct sequence name, and other time with everything translated to lower case. So, if I have 50 sequences, I see 100 sequences in the output alignment.

It seems that the error is just in outputting the alignment because 1- the output tree is fine, 2- the input alignment to the RAxML in final step in the temp directory is fine.

I will send out example test cases separately (sorry I cannot post my datasets here)!