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Commit dc06ba51 authored by Hijazi, Hussein's avatar Hijazi, Hussein
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More fixes..

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...@@ -17,20 +17,17 @@ Simulation Study ...@@ -17,20 +17,17 @@ Simulation Study
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 <num species> <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 <num species> <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
...@@ -68,16 +65,16 @@ How to run FastNet? ...@@ -68,16 +65,16 @@ How to run FastNet?
———————————— ————————————
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
2. Root ASTRAL tree: 2. Root the ASTRAL tree:
Rscript root_ASTRAL_tree.R $path $taxa $height $migration $theta $numRep Rscript root_ASTRAL_tree.R $path $taxa $height $migration $theta $numRep
3. Decompose disjoint subproblems: 3. Decompose the full set of taxa into disjoint subproblems:
Rscript generate_subproblems.R $path $taxa $height $migration $theta $numRep $subproblem_size Rscript generate_subproblems.R $path $taxa $height $migration $theta $numRep $subproblem_size
4. Create NEXUS files to run MLE: 4. Create NEXUS files for the disjoint subproblems to run MLE:
sh create_nex.sh $path $taxa $ret $genetrees sh create_nex.sh $path $taxa $ret $genetrees
5. Create datasets: for each dataset sample 1 taxon from each subproblem: 5. Create datasets: for each dataset sample 1 taxon from each subproblem:
...@@ -90,7 +87,7 @@ sh run_candidate.sh $path $taxa $ret $genetrees comb ...@@ -90,7 +87,7 @@ sh run_candidate.sh $path $taxa $ret $genetrees comb
7. Run the inference procedure on an HPCC cluster 7. Run the inference procedure on an HPCC cluster
8. Parse network and MLE scores for subproblems and candidates: 8. Parse network and MLE scores for all subproblems:
for i in `seq 0 $ret`; for i in `seq 0 $ret`;
do do
sh parse_network_subproblems.sh $path/$taxa/genetrees $i sh parse_network_subproblems.sh $path/$taxa/genetrees $i
...@@ -101,4 +98,4 @@ do ...@@ -101,4 +98,4 @@ do
Rscript select_network_Lscore_combine.R $path/$taxa/genetrees $numRep $i Rscript select_network_Lscore_combine.R $path/$taxa/genetrees $numRep $i
done done
9. Run merge.R to merge subproblems 9. Run merge.R to merge subproblems into a phylogeny
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