Updated Tutorial (markdown)

Author: heikotree

doc/Tutorial.md

@@ -81,6 +81,11 @@ This tiny alignment contains 7 DNA sequences from several animals with the seque
 >**TIP**: From version 2 you can input a directory of alignment files. IQ-TREE 2 will load and concatenate all alignments within the directory, eliminating the need for users to manually perform this step.
 {: .tip}
 
+Please note, not all characters are allowed in sequence names, because they may interfere with the structure encoding in the Newick tree files. Hence, IQ-Tree (and also other phylogenetic software) checks the names for such interfering characters and substitutes them by underscores `_`. Permitted characters in sequence names are alphanumeric letters, underscores `_`, dash `-`, dot `.`, slash `\` and vertical bar `|`. All other characters are substituted, like e.g. `hawk's-eye` is converted to `hawk_s-eye` as which it will appear in the tree.
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+Please also note, this can lead to duplicate names if you, for instance, already have two sequences named `hawk_s-eye` and `hawk's-eye`. In such cases you will obtain an error and you need to adjust the names in the original input alignment.
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+
 First running example
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