# squirrel

<% themeColor = "#419595" %>

# squirrel report ${date}

### Best-practice phylogenetics for MPXV analysis

<% section_count = 1 %> %for clade in data_for_both_clades: <%data_for_report=data_for_both_clades[clade]%>

## ${section_count}. Alignment for ${clade}

<% section_count +=1 %>

Output alignment written to ${config['outdir']}

<% figure_count = 0 %> %if config["run_phylo"]:

## ${section_count}. Tree file for ${clade}

<% section_count +=1 %>

Output tree file written to ${config['outdir']}

%if config["run_apobec3_phylo"]:

## ${section_count}. Phylo image for ${clade}

<% section_count +=1 %>
${data_for_report["phylo_svg_string"]}
<% figure_count +=1 %>

### Figure ${figure_count} | Phylogenetic tree with APOBEC3 reconstruction for ${clade}

%endif %endif %if config["seq_qc"]:

## ${section_count}. Suggested sites to mask for ${clade}

<% section_count +=1 %>

<% header = ["Name","note","present_in"] %> %for col in header:
%endfor
${col.title().replace("_"," ")}
<% import collections %> % for row in data_for_report["mask_csv"]:
%for col in header: %if col == "present_in":
%else:
%endif %endfor
${row[col].replace(";"," ")} | ${row[col]}
% endfor

%endif % endfor