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liulab
FastNet.data.scripts
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44f913da
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44f913da
authored
8 years ago
by
Hijazi, Hussein
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@@ -9,6 +9,7 @@ The following file contains information about the simulated and empirical data,
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@@ -9,6 +9,7 @@ The following file contains information about the simulated and empirical data,
Simulation Study
Simulation Study
————————————————
————————————————
1- Generate model trees using r8s.
1- Generate model trees using r8s.
2- Remove branch lengths of model trees using remove-bl.R
2- Remove branch lengths of model trees using remove-bl.R
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@@ -36,9 +37,10 @@ Rscript get_inferred_gene_trees.R
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@@ -36,9 +37,10 @@ Rscript get_inferred_gene_trees.R
Rscript get_inferred_gene_trees_with_outgroup.R
Rscript get_inferred_gene_trees_with_outgroup.R
FastNet
FastNet
____
__
_
————————
Arguments:
Arguments:
—————————
path=
\<
current path
\>
path=
\<
current path
\>
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@@ -60,7 +62,8 @@ genetrees=1000
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@@ -60,7 +62,8 @@ genetrees=1000
sample_size=1
sample_size=1
How to run FastNet?
———————————————————
1.
Run ASTRAL to get guide tree:
1.
Run ASTRAL to get guide tree:
sh run_ASTRAL.sh $path $taxa $height $migration $theta $numRep
sh run_ASTRAL.sh $path $taxa $height $migration $theta $numRep
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