add info on concatenating alignments

Author: roblanf

doc/Frequently-Asked-Questions.md

@@ -294,3 +294,24 @@ C A
 [Minh et al., 2013]: https://doi.org/10.1093/molbev/mst024
 [Ranwez et al., 2011]: https://doi.org/10.1371/journal.pone.0022594
 
+Can I use IQ-TREE to concatenate alignments?
+--------------------------------------------
+
+Yes! If you put all of your alignments you want to concatenate into a single folder, you can do this:
+
+```
+iqtree2 -p FOLDER_NAME --out-aln OUTFILE_NAME
+```
+
+This will produce:
+* OUTFILE_NAME: the concatenated alignment (default is fasta format)
+* OUTFILE_NAME.nex: the partition file in nexus format
+* OUTFILE_NAME.partitions: the partition file in RAxML format
+
+Optionally, you can add `--out-format FASTA|NEXUS` option to specify concatenated alignment format, e.g.
+
+```
+iqtree2 -p FOLDER_NAME --out-aln OUTFILE_NAME --out-format NEXUS
+```
+
+would output the alignment in nexus format.