Update README.md

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