Hi everyone, I’m now constructing the phylogenetic tree showing the relationship among cat breeds. I read the several paper about cat researches such as
Menotti-Raymond, M. et al. (2008) Patterns of molecular genetic variation among cat breeds. Genomics 91, 1–11.
Lipinski, M.J. et al. (2008) The ascent of cat breeds: genetic evaluations of breeds and worldwide random-bred populations. Genomics 91, 12–21.
Menotti-Raymond, M.A. et al. (2005) An STR forensic typing system for genetic individualization of domestic cat (Felis catus) samples. J. Forensic Sci. 50, 1061–1070.
But I can’t get information from NCBI to make the phylogenetic tree like that. If anyone has any suggestions on this field, please help me. Thank you very much for your help.
Hello Sir,
You have to look for accession number for sequences used in the papers you have mentioned or you can retrieve sequences for different cat species from NCBI ( you can use 18SrRNA sequences) and then you can use tools such as MEGA or Mesquite to align the sequences and construct your phylogenetic tree. MEGA allows you to further carry out analyses such molecular clock analysis as well.
Hope this helps.
Thanks Pankaj but cat breeds don't like virus strains, we can't look for accession number in GenBank.
If you can elaborate on the data type and source which you want to use for phylogeny , then I may provide you some more info.
Thank you Pankaj for your reply. Actually, the data type and source are come from the 2 papers that I mentioned above. Menotti-Raymond et al. (2008) showed Phylogenetic neighbor-joining tree of individuals from 38 cat breeds based on distance matrices generated from proportion of shared alleles algorithm (Dps) from composite genotypes.
If you have distance matrices then you can opt for Mesquite tool. It will suffice your requirement.
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