From d0d0d0130ef8cec03a9a62bc7f2acd84866a92ec Mon Sep 17 00:00:00 2001
From: Tomas Fer <tomas.fer@centrum.cz>
Date: Thu, 21 Jun 2018 00:07:52 +0200
Subject: [PATCH] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 27f8973..c07ec60 100644
--- a/README.md
+++ b/README.md
@@ -9,7 +9,7 @@
 1:  Processing raw reads (PhiX removal, adaptor removal, quality filtering, summary statistics)  
 2:  Mapping reads to reference (using Bowtie2/BWA), create consensus sequence  
 3:  Recognize sequences matching probes (generate PSLX files using BLAT)  
-4:  Create alignments for all genes (+ correct reading frame)  
+4:  Create alignments for all genes (+ optionally correct reading frame and/or select low heterozygosity loci)  
 5:  Treat missing data, select best genes  
 6:  Generate FastTree or RAxML gene trees + calculate/plot trees-alignment properties  
 7:  Root gene trees with outgroup, combine gene trees into a single file