Hi, I had a quick query I wonder if you could help with.
I am using iqtree to analyse non-coding regions of closely related taxa. These have enough conservation to be alignable, however often contain gaps and indels, resulting in fairly gappy alignments. Often the indels are shared between taxa, and appear to be phylogentically informative. As I understand it iqtree treats gaps as missing characters. Is it therefore not taking into account these conserved indels in phylogenetic analysis? Is there a way to get it to treat indels as informative characters? If indels are simply treated as gaps is it better to trim away indels to improve alignment quality?
Thanks, any hep is appreciated!
Sam
Hi, I had a quick query I wonder if you could help with.
I am using iqtree to analyse non-coding regions of closely related taxa. These have enough conservation to be alignable, however often contain gaps and indels, resulting in fairly gappy alignments. Often the indels are shared between taxa, and appear to be phylogentically informative. As I understand it iqtree treats gaps as missing characters. Is it therefore not taking into account these conserved indels in phylogenetic analysis? Is there a way to get it to treat indels as informative characters? If indels are simply treated as gaps is it better to trim away indels to improve alignment quality?
Thanks, any hep is appreciated!
Sam