Updated docs

Updated docs

docs/building/005_comparative_genomics.md

@@ -5,22 +5,25 @@ this is to add the species to the database, and export the protein fastas from
 CoNekT. This ensures all IDs are the same.
 
 ## Importing OrthoGroups and Gene Families
-Output from [OrthoFinder](https://github.com/davidemms/OrthoFinder) and (tribe)MCL can be directly imported, add a fitting 
-description, select the type of data you wish to import and select the file. Hit 
+Output from [OrthoFinder 1.1.x](https://github.com/davidemms/OrthoFinder/releases/tag/1.1.10) and (tribe)MCL can be directly imported. To do so, enter a description, select the type of data you wish to import and select the required file (see below). Hit 
 **Add Families** to upload the file and create the gene families in the database.
 
-For OrthoFinder, select Orthogroups.txt, from the output. For (tribe)MCL pick the 
+For OrthoFinder, select Orthogroups.txt, from the output directory. For (tribe)MCL pick the 
 file with the final output (all members of a gene family on one line).
 
 ![add_gf](../images/add_gf.png)
 
-## Importing Trees
+## Importing Trees (OrthoFinder 1.1.x only)
 
-[OrthoFinder](https://github.com/davidemms/OrthoFinder)'s phylogenetic trees can
-be imported into CoNekT. To do so **first create a gzip file** containing all the 
-trees. Furthermore you will need to locate the file **SequenceIDs.txt** which is 
+[OrthoFinder 1.1.x](https://github.com/davidemms/OrthoFinder/releases/tag/1.1.10)'s phylogenetic trees can
+be imported into CoNekT. To do so **first create a tar gzip file, with a .tgz extension** containing all the 
+**rooted** trees (and only those trees), these can be found in the **working directory** (and have the word rooted in their filenames). In linux this can be done using the [*tar* command](https://www.howtogeek.com/248780/how-to-compress-and-extract-files-using-the-tar-command-on-linux/), windows users can use [7-zip](https://www.7-zip.org/), a free tool to create archives, to create this file.
+
+Furthermore you will need to locate the file **SequenceIDs.txt** which is 
 used to convert OrthoFinder's internal IDs back to CoNekT's.
 
+Note on OrthoFinder >= 2.0: OrthoFinder 2.0 and above changed the way trees are handled and stores the trees in a different format. This is currently not supported by CoNekT.
+
 ![add_trees](../images/add_trees.png)
 
 First select the **OrthoFinder families** you wish to add trees to. Next **add a
@@ -64,3 +67,6 @@ example here:
 things : the **species**, which contain an array of short names of the species in that
 clade and a **tree** with a newick tree of that clade.
 
+## Tree Reconciliation
+
+Once trees are correctly uploaded to the database and the clades are defined, the tree reconsiliation can be started from the the admin panel's menu under : 'Build'->'Reconcile Trees'