Hi everybody! I've been tying to construct an haplotype network using TCS software (Molecular Ecology (2000) 9, 1657–1659) but I'm having problems with the input matrix. I realize that TCS was developed to infer haplotype networks from DNA sequences. However a large quantity of studies infer haplotype networks from cpSSR. How can I construct a distance matrix from cpSSR when I only have the allele sizes? or can I use a matrix with the "raw" data from the cpSSR?
Thank you in advance!
Hola, yo creo que solo necesitas el archivo de alineamiento de tus secuencias en formato fasta, .fas. De lo demás no tengo mucha idea de que es a lo que te refieras exactamente.
Saludos,
Hi, I think you just need to input file your alignment data in FASTA format, .fas. Of the rest I have no idea what question that you refer.
Regards,
Cristian
Dear Alfredo:
If you know the mutations involved in your cpSSR allele size variations (and that they are restricted to the microsatellite motif) you can transform then into a virtual sequence and then construct a fasta file to analyse it with TCSconsidering gaps as a fith state.
Example you have three samples with sizes 101, 102, 103 corresponding to a (A)n microsatellite. then you can build a sequence matrix that would be:
Sample 1: A--
Sample 2: AA-
Sample 3: AAA
Hope this is of help.
Best regards
José Gabriel Segarra
Thank you very much for your answers,
I attach a paper where haplotype network was constructed using cpSSR. As you may see, the methods are not informative. They just mention that TCS was used to construct the haplotype network and nothing more.
I found in the TCS' documentation that a distance matrix may be used as the input file. I am now constructing an haplotype distance matrix, where the distance between two haplotypes is the total difference in length between haplotypes... I hope this work
José Gabriel, that's a good idea, I will try that either. I appreciate your time
Thank you very much Artur!
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