How the gaps (in aligned sequences of species) are interpreted by the final program for phylogenetic analysis may change the results depending on whether you code the gaps as "missing data" = ? or as containing some information. Probably the safest way to look at this is to delete the region for the missing data in one analysis, and leave it as is in another analysis, then compare your results. We use Mesquite to input our sequences and manipulate gaps, etc, then we can align, then export to MEGA or to TNT or some other program for analysis. Hope that this helps. Scott

Hi,

As mentioned above by Dr. Gardner...gaps if not programmed to be recognised as 'missing data' may  be taken as deletions....and the sequences containing such end gaps may apparently look as highly divergent..The best way is to use similar length sequences for alignment first...edit the alignment if needed and then use for inferring phylogeny...In addition, use multiple algorithms, more than one loci, and never forget statistical analysis of the data and tree

bye

Hi,

The way MEGA deal with gaps rely on the option selected in the "Gaps/missing data treatment" box in the analysis preferences menu. This is the paragraph about gaps in the Help option present in MEGA;

"You may choose to remove all sites containing alignment gaps and missing information before the calculation begins (Complete-deletion option). Alternatively, you may choose to retain all such sites initially, excluding them as necessary in the pairwise distance estimation (Pairwise-deletion option), or you may use Partial Deletion (Site coverage) as a percentage."

So, you can try different options and compare your results.

Good Luck