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nclark-lab / RERconverge

Analysis of convergence between organismal traits and DNA/protein sequences
GNU General Public License v3.0
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Does the paralog genes from the same gene tree affect the output? #51

Closed hongzhonglu closed 4 years ago

hongzhonglu commented 4 years ago

Hi, could I ask a question? In my analysis, I found for some ortholog gene groups, the paralog genes existed for some species, does it affect the evolution rate analysis?

nclark-lab commented 4 years ago

This is an important question. It is important to stringently filter out paralogous sequences from the alignments to the best that is possible. They have been seen to diminish signals in important correlations. They could also potentially create false positive correlations. Some potential methods to identify strictly orthologous groups are InParanoid and whole genome alignments that use synteny (blastz chain alignments). Best of luck with your analysis!

hongzhonglu commented 4 years ago

@nclark-lab Great thanks for your help!