Update README.md

README.md

@@ -3,16 +3,16 @@
 Set of bash scripts for analysis of HybSeq raw data. Consists of several steps:   
 
 
-0. Download FASTQ files from Illumina BaseSpace storage  
-1. Processing raw reads (PhiX removal, adaptor removal, quality filtering, summary statistics)  
-2. Mapping reads to reference (using Bowtie), create consensus sequence  
-3. Recognize sequences matching probes (generate PSLX files using BLAT)  
-4. Create alignments for all genes  
-5. Treat missing data, select best genes  
-6. Generate FastTree or RAxML gene trees + trees-alignment properties  
-7. Root gene trees with outgroup, combine gene trees into a single file  
-8. Estimate species tree (ASTRAL, ASTRID, MRL, concatenation)  
-9. Subselect suitable genes and repeat steps 6+7 
+0: Download FASTQ files from Illumina BaseSpace storage  
+1: Processing raw reads (PhiX removal, adaptor removal, quality filtering, summary statistics)  
+2: Mapping reads to reference (using Bowtie), create consensus sequence  
+3: Recognize sequences matching probes (generate PSLX files using BLAT)  
+4: Create alignments for all genes  
+5: Treat missing data, select best genes  
+6: Generate FastTree or RAxML gene trees + trees-alignment properties  
+7: Root gene trees with outgroup, combine gene trees into a single file  
+8: Estimate species tree (ASTRAL, ASTRID, MRL, concatenation)  
+9: Subselect suitable genes and repeat steps 7+8 
 
 Uses many additional software that must be installed and put in the PATH prior to run scripts (see Table located in docs folder and consider to run install_software.sh).  
 Also utilizes many scripts developed by others (located in HybSeqSource folder). PLEASE CITE APPROPRIATELY THOSE SCRIPTS WHEN USING HybPhyloMaker!