Can SATe output distance matrix?

[yumeng wang]

Hi,

Just a quick question: Is there any option for distance matrix output in SATe, or some quick modification on scripts that can give me the distance matrix? Thank you very much for your help.

Best,

Yumeng

[Jamie Oaks]

Hi Yumeng,

Thank you for your post. The short answer is no; SATe has no internal
representation of a distance matrix during an analysis. However, if you
want distances based on an alignment and/or tree, you certainly can use
an alignment/tree estimated by SATe to calculate the distances in some
other software (DendroPy comes to mind for calculating patristic
distances, but I am sure there a lot of other options out there). If you
want distances from the unaligned sequences, SATe will not be of use to
you. You would be better off using another tool, like the "showdist"
command in PAUP (there are probably free software options too).

I hope this helps!

Cheers,

Jamie

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--
Jamie Oaks
Biodiversity Institute
Department of Ecology & Evolutionary Biology
University of Kansas
Dyche Hall, 1345 Jayhawk Blvd
Lawrence, KS 66045-7561

Office Phone: 785-864-3439
Office Fax: 785-864-5335
E-mail: joa...@ku.edu

[yumeng wang]

Thanks a lot!

2013/5/8 Jamie Oaks <joa...@gmail.com>

Hi Yumeng,

Thank you for your post. The short answer is no; SATe has no internal representation of a distance matrix during an analysis. However, if you want distances based on an alignment and/or tree, you certainly can use an alignment/tree estimated by SATe to calculate the distances in some other software (DendroPy comes to mind for calculating patristic distances, but I am sure there a lot of other options out there). If you want distances from the unaligned sequences, SATe will not be of use to you. You would be better off using another tool, like the "showdist" command in PAUP (there are probably free software options too).

I hope this helps!

Cheers,

Jamie

On 05/07/2013 04:13 PM, yumeng wang wrote:

Hi,

Just a quick question: Is there any option for distance matrix output in SATe, or some quick modification on scripts that can give me the distance matrix? Thank you very much for your help.

Best,
Yumeng

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--
Jamie Oaks
Biodiversity Institute
Department of Ecology & Evolutionary Biology
University of Kansas
Dyche Hall, 1345 Jayhawk Blvd
Lawrence, KS 66045-7561

Office Phone:  785-864-3439
Office Fax:  785-864-5335
E-mail:  joa...@ku.edu

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Yumeng Wang

Graduate Student

Structural and Computational Biology and Molecular Biophysics

Baylor College of Medicine

Houston, Texas 77030