How does IQ-TREE calculate degree of missing data?

[veronicamb]

Hello everyone,

I was wondering how iqtree calculates the degree of missing data in a dataset. It clearly is influenced by the partitioning scheme, but I don't quite understand how.

Is this something I can find in the manual online (when the website is back up!)?

Thanks!

Veronica

[bqminh]

I've moved this to discussion instead of issue page.
Missing data are defined as -, N, ?, X, etc. characters in the alignment (http://www.iqtree.org/doc/Frequently-Asked-Questions#how-does-iq-tree-treat-gapmissingambiguous-characters). IQ-TREE simply counts the fraction of them in the alignment. If you have a partitioned alignment, where certain taxon doesn't have sequence for a certain partition, then this is also counted as missing data.
Does that answer your question?