Non-coding sequences like ITS or introns often demonstrate considerable differences even among closely related species, many or most of those representing indels. The latter seem to be excluded from analysis by programs like MEGA or MrBayes. Are there some more or less standard tools that consider indels in the assessment of phylogenetic distances?
One problem is that there are several types of in/dels and it is not easy to code them differently and write software to deal with those codes. A 9 base insertion that is a duplication of the 9 bases next to it should be treated differently than a 9 base insertion of random DNA. Gain and loss of bases in repeat elements (ATATATATATAT or GGGGGGG) is different than at other sites. Insertions of ALU repeats or transposons is different than addition of a new intron within an exon.
It could be possible to replace the --- characters needed to make the alignment with NNN for one type of in/del and with XXX for another, and so on, but then we need to modify the phylogenetic reconstruction program to deal with the new codes.
WIth DNA sequencing so inexpensive today, it makes more sense to gather more data, than to try to squeak more information out of problematic parts of the data we have.
Any phylogenetic inference program that is not deleting positions with gaps will, in a way or another, capture some phylogenetic signal contained in those positions with gaps, although deletion/insertion events are not included in the sequence evolution models.
You can do it even in MEGA choosing the partial deletion options and 5% (smallest) site coverage cut off. It will include practicly every sites if you have a couple of sequences .
PhyML (online at http://www.phylogeny.fr) will do it as well, just you should clear the check-box before "remove gaps from alignment" in the advanced settings.
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