Hello, I am researching the phylogenetic tree of snakes. (bayesian Inference tree)
My sequences are 1300 bp, but sequences of outgroups are about 600 bp.
Can I change the difference of about 700bp to missing data and analyze it?
Since there is no appropriate length between related species,
I tried using outgroup with a long distance, but the resolution is poor.
Do I need to cut off the non-overlapping area before using it?
Overall, since you are interested in the relationships among the members of the ingroup (the outgroup is assumed to be outside), then you are better off with missing data there than you are if you have a lot of missing data among the ingroup taxa. The really tricky problem is when you have complementary patterns of missing data, such as
agctagct--------
--------agctagct
Many of the phylogenetic programs will view these two taxa as identical, because missing character states are treated as a wild card that is considered to be the same as the character state of a taxon it is compared to. This is definitely something to avoid. See Cladistics 34:467 (2018) for an example.
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