Merge branch 'master' of https://github.com/davidemms/STAG

README.md

@@ -1,11 +1,16 @@
-# STAG: Species Tree from All Genes
+# STAG: Species Tree inference from All Genes
 
 ![STAG logo](stag_logo.png)
 
-STAG is a LINUX tool for inferring a species tree from a set of gene trees. Its major advantage is that it can use all gene families as input to the species tree inference rather than just one-to-one orthologues that almost all other methods are limited to. In many cases this provides significantly more data on which to base species tree inference. A second advantage is that the user does not need to select the genes to be used for species tree inference. It can take as input the directory of all gene trees for a set of species and it will use those trees that are appropriate.
+STAG is a method for inferring a species tree from a set of gene trees. It can use gene trees inferred from any gene family that contains all the species under consideration. These gene familes can contain paralogues, co-orthologues, or any number of gene duplcation events, and thus STAG is not limited to analysis of gene trees inferred from sets of one-to-one orthologues. This ability to use paralogous gene families enables the use of substantially more data from which to base species tree inference. 
+
+### Additional Advantages of Using STAG
+1. STAG trees have realistic branch lengths that can be used for downstream analyses.
+2. STAG trees have support values that summarise the fraction of trees that support each bipartition.
+3. STAG is fast and memory efficient.
 
 ### Installation:
-STAG can just be downloaded from the 'Releases' tab and run without needing to be installed but it requires the FastME program to be installed or in the system path.
+STAG is written in python and can be downloaded from the 'Releases' tab. It is designed to work on Linux operating systems and can be run directly without needing to be installed. STAG requires the FastME program to be installed and in your system path.
 
 #### FastME
 FastME can be obtained from http://www.atgc-montpellier.fr/fastme/binaries.php. The package contains a 'binaries/' directory. Choose the appropriate one for your system and copy it to somewhere in the system path e.g. '/usr/local/bin'** and name it 'fastme'. E.g.:
@@ -25,13 +30,13 @@ Examined 10784 trees
 
 STAG species tree: /home/david/workspace/git/STAG/stag/ExampleData/STAG_ResultsFeb02/SpeciesTree.tre
 ```
-
-The species tree is unrooted and has branch lengths and supported values calculated from the input gene trees. You can use your gene trees to root the species tree using https://github.com/davidemms/STRIDE:
+### Rooting STAG Trees
+The tree produced by STAG is unrooted. However, following STAG tree inference the same set of trees used by STAG can be used to root the STAG tree using STRIDE. https://github.com/davidemms/STRIDE: Using the example dataset above the you would root the STAG tree using STRIDE using the following command.
 
 `python ../STRIDE/stride/stride.py -s second_dash -S /home/david/workspace/git/STAG/stag/STAG_ResultsFeb02_1/SpeciesTree.tre -d stag/Fungi_Gene_Trees/`
 
-### OrthoFinder Integration:
-The best way to generate the complete set of gene trees for your species is with OrthoFinder: https://github.com/davidemms/OrthoFinder/
+### Generating Input Datasets for STAG:
+The best way to generate a set of gene trees for your species is with OrthoFinder: https://github.com/davidemms/OrthoFinder/
 
 STAG is designed to work with OrthoFinder output. Instead of preparing at species map file you can jsut use the SpeciesIDs.txt file found in the OrthoFinder WorkingDirectory. E.g.
 `python stag.py ExampleData/Fungi_SpeciesIDs.txt ExampleData/Fungi_Gene_Trees/`