Problem with second run

[Suman Neupane]

Hi,

I have problem executing "Uncheck the box in “Initial alignment" command after my first run. Whenever I upload my fasta file for the first time, the box is  already deactivated and unchecked . I am using Windows with 64-bit operating system with intel core i5 cpu. I can send you my dataset if you want to have a look.

I am also attaching a screenshot of what it looks like when I upload the data

Thank you,

Suman Neupane,

Department of Biological Sciences, 
Old Dominion University,
45th Street, 110 Mills Godwin Building,
Norfolk, Virginia 23529-0266
U.S.A

[Jamie Oaks]

Hi Suman,

The SATe GUI should only let you check that box if all the sequences in your input file are the same length.  By checking the "use for initial tree" box, you are telling SATe to treat your sequences as aligned, and to bypass the initial alignment step.  If the sequences are not the same length, the GUI does not let you check this box, because it assumes the sequences are not aligned.

Please check that all your sequences are the same length.  If they are, and SATe still will not allow you to check the "use for initial tree" box, please let us know.  You can send your dataset off-list to joa...@ku.edu or mtho...@ku.edu.  We will keep your data confidential and only use it to diagnose the problem.

Thanks you for reporting the problem.

Cheers,

Jamie

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