Update help

davidemms · Dec 16, 2016 · 4b97dba · 4b97dba
1 parent e031179
commit 4b97dba
Showing 1 changed file with 12 additions and 3 deletions.
diff --git a/Tests/test_orthofinder.py b/Tests/test_orthofinder.py
@@ -76,12 +76,18 @@
 
 Control where analysis stops (optional):
 
--og, --only-groups
-    Only infer orthogroups, do not infer gene trees of orthologues.
-
 -op, --only-prepare
     Only prepare the BLAST input files in the format required by OrthoFinder.
 
+-og, --only-groups
+    Stop after inferring orthogroups, do not infer gene trees of orthologues.
+
+-os, --only-seqs
+    Stop after inferring orthogroups and writing out sequence files for each orthogroup
+
+-ot, --only-trees
+    Stop after inferring gene trees, do not infer orthologues.
+
 Additional arguments:
 
 -t n_blast_threads, --threads n_blast_threads
@@ -91,6 +97,9 @@
     The number of threads to use for the less readily parallelised parts of the OrthoFinder algorithm.
     There are speed/memory trade-offs involved, see manual for details. [Default is 1]
 
+-M tree_inference_method, --method tree_inference_method
+    Use tree_inference_method for gene trees. Valid options are 'dendroblast' & 'msa'. [Default is dendroblast]
+
 -I inflation_parameter, --inflation inflation_parameter
     Specify a non-default inflation parameter for MCL. Not recommended. [Default is 1.5]