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Podosporaceae_config.yaml
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Podosporaceae_config.yaml
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# Configuration file of the Podosporaceae.smk pipeline
## Master nexus file
masternex: "data/Podosporaceae_20200602.nxs"
## Name of the full concatenation of all markers in the master nexus file
allmarkersname: "allmarkers"
## RAxML-like partition file to calculate the SLS and GLS metrics (It must be named "{allmarkersname}_combining_orders.txt")
orders: "data/allmarkers_combining_orders.txt"
## Filtering for alignments of individual markers
minfrac: 0.45 # min fraction of overlap with the whole alignment length for a sequence to be considered
minlen: 250
## Scripts
sitewise_analyzer: "scripts/1_sitewise_analyzer.pl"
genewise_analyzer: "scripts/2_genewise_analyzer.pl"
plotShen: "scripts/Shen2017_podofam.R"
# Outgroup clade
outgroup: ["Lasiosphaeria_ovina_SMH1538", "Zopfiella_tabulata_CBS230.78", "Sordaria_fimicola_SMH4106", "Diplogelasinospora_princeps_FMR13414", "Chaetomium_globosum_CBS148.51", 'Chaetomium_globosum_CBS160.62', 'Cercophora_mirabilis_CBS120402']
# A representative of clades A, B and C in that order
testmonophyly: ["Podospora_anserina_S", "Cercophora_grandiuscula_CBS120013", "Podospora_fimiseda_CBS990.96"]