handling polytomies

docs/mds/faq.md

@@ -1,6 +1,33 @@
 Frequently asked questions
 
+## How does Physcraper handle polytomies of starting trees?
 
-# Polytomies
+The Physcraper starting tree is a phylogeny whose tip labels must have been standardized to the OpenTree Taxonomy (as described in the Introduction section:
+[Mapping names to taxa](https://physcraper.readthedocs.io/en/latest/how_to_start.html#updating-your-own-tree-and-alignment)).
+Original tip labels of the starting tree must be identical to taxon labels on the starting alignment.
+However, not all taxon labels in the alignment have to be present in the tree and
+visceversa.
 
-How does Physcraper handle polytomies?
+Physcraper makes use of the starting tree in four main ways:
+1. to delimit a taxon for the GenBank search (a search taxon),
+2. to be used as starting tree for the phylogenetic reconstruction software of choice,
+3. to standardize the taxon names from the starting alignment, and
+4. to compare the updated phylogenetic relationships with the original ones.
+
+
+Physcraper does not really "handle" polytomies. The goal of the software is to use the
+existing phylogenetic information that has been generated, reviewed, published and curated by experts in the field.
+
+If a starting tree contains polytomies, these can only affect the outcome of the analysis if the starting tree is used for the case (1) delimiting a taxon for the GenBank search.
+To delimit the search taxon from the starting tree, a known outgroup is necessary.
+The outgroup can be user defined. If the outgroup is not defined by the user, Physcraper will attempt to root the starting tree following the OpenTree Taxonomy.
+If succesful, it will take the tip labels from the earliest diverging branch with the least number of tips. These will be used as outgroup. However, if the starting tree has polytomies
+around the early diverging branches,
+the automatic rooting is problematic and can have multiple solutions.
+
+
+
+## How does Physcraper use the starting alignment?
+
+Physcraper uses the input DNA alignment (single or multiple marker) to mine the GenBank database with the goal of increasing the
+lineage sampling of the alignment within a given biological group.