Fasta files & alignment issues

[Patricia Sanchez-Baracaldo]

Hi there (Jamie still there?), 

I am analysing a new data set (with has grown from last year) and I am getting weird trees - meaning I know some of the phylogenetic relationships (groupings) are wrong. 

Also when I look a the alignments (output) - homologs sites clearly don't match (align). 

The only thing that I can think it is different is that the column width for sequences in my fasta files. 

I have added some new sequences - and the width is different. 

Perhaps I would need to send you an example to explain.  

Let me know - so I can send more information. 

I am looking forward to hearing if you have experienced this problem before, 

Many thanks, 

Regards, 

Patricia

[Jamie Oaks]

Hi Patricia,

Yes, still here!

If you want to send me some examples that would be great (you can send
them off-list to joa...@gmail.com). Also, if you could provide some more
details about your analyses, hopefully we can figure out the issue. For
example, what version of SATe are you using? Is it the same version you
used before you added more data (when your results were less weird)?
What is your general data structure (i.e., number of individuals, loci,
average locus length, etc.)? What are your analysis settings? Providing
the configuration file would help for this.

Hopefully we can figure out whether this is a SATe or data issue, and if
the former, find a solution.

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

[Tandy Warnow]

Are the sequences all full-length?

Tandy

On Wed, Jun 12, 2013 at 3:35 PM, Jamie Oaks <joa...@gmail.com> wrote:

Hi Patricia,

Yes, still here!

If you want to send me some examples that would be great (you can send them off-list to joa...@gmail.com). Also, if you could provide some more details about your analyses, hopefully we can figure out the issue. For example, what version of SATe are you using? Is it the same version you used before you added more data (when your results were less weird)? What is your general data structure (i.e., number of individuals, loci, average locus length, etc.)? What are your analysis settings? Providing the configuration file would help for this.

Hopefully we can figure out whether this is a SATe or data issue, and if the former, find a solution.

Cheers,

Jamie

On 06/12/2013 04:04 AM, Patricia Sanchez-Baracaldo wrote:

Hi there (Jamie still there?),

I am analysing a new data set (with has grown from last year) and I am getting weird trees - meaning I know some of the phylogenetic relationships (groupings) are wrong.

Also when I look a the alignments (output) - homologs sites clearly don't match (align).

The only thing that I can think it is different is that the column width for sequences in my fasta files.
I have added some new sequences - and the width is different.

Perhaps I would need to send you an example to explain.

Let me know - so I can send more information.

I am looking forward to hearing if you have experienced this problem before,

Many thanks,

Regards,
Patricia


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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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