SimPhy configuration scripts for simulations reported in the study titled: Species tree inference methods intended to deal with incomplete lineage sorting are robust to the presence of paralogs

Luay Nakhleh
Many recent phylogenetic methods have focused on accurately inferring species trees when there is gene tree discordance due to incomplete lineage sorting (ILS). For almost all of these methods, and for phylogenetic methods in general, the data for each locus is assumed to consist of orthologous, single-copy sequences. Loci that are present in more than a single copy in any of the studied genomes are excluded from the data. These steps greatly reduce the number...
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2 downloads reported since publication in 2021.

These counts follow the COUNTER Code of Practice, meaning that Internet robots and repeats within a certain time frame are excluded.
What does this mean?