Has anyone worked with treeSAAP (Selection on Amino Acid Properties) software? I am having problems while opening files using the software. It is not showing the 'tree' file. I think I have made mistakes in the format of the file. So please send me a sample format which I can follow and implement in my sequences.
David McClellan has uploaded a very helpful video on Youtube on how to input an alignment and tree into TreeSAAP. Once you have an alignment you will need to make the following amendments to your FASTA file:
#NEXUS
BEGIN DATA;
format noninterleave datatype: DNA
matrix
Sample_1
AACATTTCATCATGATGAAATTTTGGCTCTCTACTAGGAATCTGCTTAATTCTAC...…ATCCTAGTACTTATACCAATTACCAGCACAATCGAAAATAATCTCCTAAAATGA
;
END;
Begin trees;
tree ExampleTree = [&U]((((((((((((((((((((((((((((((((Taxa1,Taxa2),...
…,(Taxa10,(Taxa11,(Taxa12,Taxa13)))))))))))))))))));
END;
I recognize that this is a very late response to the question but hopefully this will help with future inquiries.
http://www.youtube.com/watch?v=_AcBzfjFuGA
The file is in both text and fasta format. But, actually I am asking for the sample format of the sequence file to be used in the treeSAAP.
sorry, i'm not working on it, but if in future i'll defiantly inform you.
David McClellan has uploaded a very helpful video on Youtube on how to input an alignment and tree into TreeSAAP. Once you have an alignment you will need to make the following amendments to your FASTA file:
#NEXUS
BEGIN DATA;
format noninterleave datatype: DNA
matrix
Sample_1
AACATTTCATCATGATGAAATTTTGGCTCTCTACTAGGAATCTGCTTAATTCTAC...…ATCCTAGTACTTATACCAATTACCAGCACAATCGAAAATAATCTCCTAAAATGA
;
END;
Begin trees;
tree ExampleTree = [&U]((((((((((((((((((((((((((((((((Taxa1,Taxa2),...
…,(Taxa10,(Taxa11,(Taxa12,Taxa13)))))))))))))))))));
END;
I recognize that this is a very late response to the question but hopefully this will help with future inquiries.
http://www.youtube.com/watch?v=_AcBzfjFuGA
Yes, we use TreeSAAP routinely. Do you still need help? Here's an example of the results usage in a publication.
Article Functional Validation of Hydrophobic Adaptation to Physiolog...
Hi everybody,
How to use treesaap, in linux shell for thousands genes and multiples species.
Are there some examples and scripts to use it?
Thanks
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