update 230724

materials/12-phylogenetics.md

@@ -186,7 +186,7 @@ mkdir results/iqtree
 
 # run iqtree2
 iqtree \
-  -s results/snp-sites/core_gene_alignment_snps.aln \
+  -s results/snp-sites/aligned_pseudogenomes_masked.fas \
   -fconst 692240,1310839,1306835,691662 \
   --prefix results/iqtree/Nam_TB \
   -nt AUTO \
@@ -297,7 +297,7 @@ The main file of interest is `Nam_TB.treefile`, which contains our tree in the s
 
 ### Rooting a phylogenetic tree
 
-Rooting a phylogenetic tree is essential for making sense of evolutionary relationships and for providing a temporal context to the diversification of species. It transforms an unrooted tree, which simply shows relationships without direction, into a meaningful representation of evolutionary history. The most common way to accurately root a phylogenetic tree is to include an outgroup that is known to be more distantly related to the taxa included as part of the analysis. In our example we mapped our TB sequences to the MTBC0 reference, which is an outgroup to all members of the MTBC, so we'll use this to root our tree before visualizing it.  There are a few different tools that could be used to root a phylogenetic tree but we've provided a python script, `root_tree.py` to do this. You can run the script using the following command:
+Rooting a phylogenetic tree is essential for making sense of evolutionary relationships and for providing a temporal context to the diversification of species. It transforms an unrooted tree, which simply shows relationships without direction, into a meaningful representation of evolutionary history. The most common way to accurately root a phylogenetic tree is to include an outgroup that is known to be more distantly related to the taxa included as part of the analysis. In our example we mapped our TB sequences to the MTBC0 reference, which is an outgroup to all members of the MTBC, so we'll use this to root our tree before visualizing it.  There are a few different tools that could be used to root a phylogenetic tree but we've provided a python script, `root_tree.py` to do this. You can run the script using the following command (we're going to root the tree we've provided in the **preprocessed** directory so you don't need to edit the command):
 
 ```bash
 python scripts/root_tree.py -i preprocessed/iqtree/Nam_TB.treefile -g MTBC0 -o Nam_TB_rooted.treefile