Updated Frequently Asked Questions (markdown)

Author: heikotree

doc/Frequently-Asked-Questions.md

@@ -85,8 +85,7 @@ How does IQ-TREE treat gap/missing/ambiguous characters?
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 Gaps (`-`) and missing characters (`?` or `N` for DNA alignments) are treated in the same way as `unknown` characters, which represent no information. The same treatment holds for many other ML software (e.g., RAxML, PhyML). More explicitly,
-for a site (column) of an alignment containing `AC-AG-A` (i.e. A for sequence 1, C for sequence 2, `-` for sequence 3, and so on), the site-likelihood
-of a tree T is equal to the site-likelihood of the subtree of T restricted to those sequences containing non-gap characters (`ACAGA`).
+for a site (column) of an alignment containing `AC-AG-A` (i.e. A for sequence 1, C for sequence 2, `-` for sequence 3, and so on), the site-likelihood of a tree T is equal to the site-likelihood of the subtree of T restricted to those sequences containing non-gap characters (`ACAGA`).
 
 Ambiguous characters that represent more than one character are also supported: each represented character will have equal likelihood. For DNA the following ambigous nucleotides are supported according to [IUPAC nomenclature](https://en.wikipedia.org/wiki/Nucleic_acid_notation):
 
@@ -102,17 +101,20 @@ Ambiguous characters that represent more than one character are also supported:
 | H    | A, C or T (next letter after G) |
 | D    | A, G or T (next letter after C) |
 | V    | A, G or C (next letter after T) |
-| ?, -, ., ~, O, N, X | A, G, C or T (unknown; all 4 nucleotides are equally likely) |
+| ?, -, ., ~, !, O, N, X | A, G, C or T (unknown; all 4 nucleotides are equally likely) |
 
-For protein the following ambiguous amino-acids are supported:
+For protein sequences the following ambiguous amino-acids are supported:
 
 | Amino-acid | Meaning |
 |------------|---------------------------------------------------------------|
 | B          | N or D |
 | Z          | Q or E |
 | J          | I or L |
 | U          | unknown AA (although it is the 21st AA) |
-| ?, -, ., ~, * or X | unknown AA (all 20 AAs are equally likely) |
+| ?, -, ., ~, *, ! or X | unknown AA (all 20 AAs are equally likely) |
+
+The letters `*` and `!` may found in alignments of protein and/or coding DNA sequences. 
+Stop codon is typically translated to `*`. Some alignment programs also mark frameshift mutations (cf. [Ranwez et al., 2011]), that means since frameshift mutations in a codon alignment cause incomplete codons that cannot be unambiguously translated the resulting position in the translated protein sequence and padding positions in the respective codon are marked using `!`. 
 
 
 Can I mix DNA and protein data in a partitioned analysis?