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controlfile.tbsc
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controlfile.tbsc
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# Transmic control file
# Please only edit parameter values within double quotes.
# ------------------------------------------------------
# Clustering parameters
# 1.Name of the tree file
# (or absolute path if file not in same directory as the programm)
#tree_file="RAxML_bipartitions_WithFP.BS_TREE"
tree_file="/home/mi/yoocef/Dropbox/projects2016/SubtypA_Kirsten/pureA1_gtr_ucln_skygrid_treeannotator2.trees"
# 2.Tree format (newick/nexus)
tree_format = "nexus"
# 3.Node support (bootstrap/posterior)
node_support = "posterior"
# 4.Cut-off value for the mean pairwise patristic distances (mppd)
# i.e. a clade is a transmission cluster if mppd =< cutoff_mppd
#type here one numeric value or a range between x and y in z-steps by typing x:z:y
#cutoff_mppd="0.001:0.0005:0.003"
cutoff_mppd="10:10:100"
# 5.Cut-off for the node support value (bootstrap or posterior, in percent)
# i.e. a clade is a transmission cluster if support >= cutoff_node_support
#type here one numeric value or a range between x and y in z-steps by typing x:z:y
#cutoff_node_support="80:5:100"
cutoff_node_support="95"
# 6.Patient-wise clustering (true/false)
# This option only works with sequence identifiers consisting
# of a unique sequence ID followed by a patient ID separated by
# an underscore e.g. seqID_patID. In this case set it to true.
# In all other cases (e.g. simple sequence-based clustering) set this
# option to false.
patWiseClust="false"
# 7.Name of excel file with patient meta-information
# The first column of this excel file must contain the sequence-IDs
# of the taxa in the tree file. The following columns contain additional
# information for each sequence. If
# If no file with meta-information available, leave this empty: "".
#database_file="RKIdatabase.xls"
database_file=""
# 8.Identifier of the outgroup sequence
outgroupSeqId="SIVcpz_ant"
#outgroupSeqId=""
#---------------------------------------
# Visualization
#
# 9. Figure showing distribution of patristic distances between taxa (true/false)
# Set to true to generate a plot.
figure_distances="true"
# 10. Figure showing number of clusters depending
# on distance and support thresholds (true/false)
# Set to true to generate a plot.
figure_nr_clusters="true"
# 11. Figure showing mean size of clusters depending
# on distance and support thresholds (true/false)
# Set to true to generate a plot.
figure_sizeof_clusters="true"