Monophy : screening tree files for detection of local adaptations
online resourceposted on 25.04.2019, 19:09 authored by yves terratyves terrat
Monophy is a standalone perl written program used to detect local adaptations in large datasets of genes trees.
Genes from different organisms should be first classified into ortholog groups using Roary, OrthoFinder or OrthoMCL.
Ortholog group are further individually aligned and a tree is generated for each group (this analysis should include bootstrap or posterior probability values).
Then, Monophy uses as inputs nexus trees, and a metadata file which indicates the geographical origin of each sample (encoded by digits).
The parameters could be adjusted to modify the stringency of analysis.
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