The genetrees used in the simulation study are located in the following folders:
The genetrees/scripts used in this study are located in the following folders:
1- inferred-non-deep-model-conditions: contains inferred genetrees using non-deep gene flow model conditions. This folder also contains folders named \<number of taxa\>-\<number of reticualtions\>. For example; 15-1 folder contains genetrees that were used to infer a network with 15 taxa and a single reticulation. We also add genetrees used by each method (i.e. mle or mle-length or mpl).
1- inferred-non-deep-model-conditions: contains inferred genetrees using non-deep gene flow model conditions. This folder also contains folders named \<number of taxa\>-\<number of reticulations\>. For example; 15-1 folder contains genetrees that were used to infer a network with 15 taxa and a single reticulation. We also add genetrees used by each method (i.e. mle or mle-length or mpl).
2- inferred-vary-loci: contains inferred genetrees using non-deep gene flow model conditions where we vary the number of loci from 100 to 1000.
2- inferred-vary-loci: contains inferred genetrees using non-deep gene flow model conditions where we vary the number of loci from 100 to 1000.
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@@ -26,5 +26,5 @@ The genetrees used in the simulation study are located in the following folders:
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@@ -26,5 +26,5 @@ The genetrees used in the simulation study are located in the following folders:
6- yeast-dataset: contains inferred genetrees used in the yeast analysis.
6- yeast-dataset: contains inferred genetrees used in the yeast analysis.
7- sciprts: contains scripts used by FastNet to infer a species network. run.sh is a wrapper script that controls the execution of the other scripts. The parameters used by FastNet can be changed in this master script.
7- scripts: contains scripts used by FastNet to infer a species network. run.sh is a wrapper script that controls the execution of the other scripts. The parameters used by FastNet can be changed in this master script.