2- Remove branch lengths of model trees using remove-bl.R
2- Remove branch lengths of model trees using remove-bl.R
3- simulate.R, simulate-ret.R, random_network.R
3- simulate.R, simulate-ret.R, random_network.R
These R scripts take an input of model trees simulated by r8s and generates the model network ms command
These R scripts take an input of model trees simulated by r8s and generate the model network ms command
4- Run the following command to parse the true gene trees:
4- Run the following command to parse the true gene trees:
sh parse_gene_trees.sh <numspecies><height><migration_rate><theta><numRep>
sh parse_gene_trees.sh \<num species\>\<height\> <\migration_rate\>\<theta\>\<numRep\>
5- Run the sequence evolution program using the following script:
5- run_seq_gen.sh is a bash file that simulates DNA sequence
sh run_seq_gen.sh <numspecies><height><migration_rate><theta><numRep>
run_seq_gen.sh is a bash file that simulates DNA sequence
evolution using seq-gen from a set of gene trees generated by ms.
evolution using seq-gen from a set of gene trees generated by ms.
To run it, use the following command: sh run_seq_gen.sh \<num species\>\<height\>\<migration_rate\>\<theta\>\<number of replicates\>
To run it, use the following command: sh run_seq_gen.sh \<num species\>\<height\>\<migration_rate\>\<theta\>\<number of replicates\>
where theta is \<0.08\>. The output of seq-gen is stored in the following folder seqgen_\<theta>. In seqgen_\<theta\>, seq_\<height of model phylogeny\>_\<number of taxa\>_\<replicate #\>.txt contains the sequence alignment for each marker.
where theta is \<0.08\>.
6- run_parse.sh
6- run_parse.sh is a bash file that parses sequence alignments generated by seq-gen, and use them as input to FastTree to infer a gene tree for each DNA sequence alignment. To run it, use the following command: sh run_parse.sh \<num species\>\<height of model phylogeny\>\<migration_rate\>\<theta\>\<number of replicates\>
a bash file that parses sequence alignments generated by seq-gen, and use them as input to FastTree to infer a gene tree for each DNA sequence alignment. To run it, use the following command: sh run_parse.sh \<num species\>\<height of model phylogeny\>\<migration_rate\>\<theta\>\<number of replicates\>
7- Run the following script to get the gene trees without the outgroup:
7- Run the following script to get the gene trees without the outgroup:
Rscript get_inferred_gene_trees.R
Rscript get_inferred_gene_trees.R
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@@ -68,16 +65,16 @@ How to run FastNet?
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@@ -68,16 +65,16 @@ How to run FastNet?
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1. Run ASTRAL to get guide tree:
1. Run ASTRAL to get a guide tree:
sh run_ASTRAL.sh $path $taxa $height $migration $theta $numRep
sh run_ASTRAL.sh $path $taxa $height $migration $theta $numRep