More fixes..

README.md

@@ -17,20 +17,17 @@ Simulation Study
 2- Remove branch lengths of model trees using remove-bl.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:
-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: 
-sh run_seq_gen.sh <num species> <height> <migration_rate> <theta> <numRep>
-run_seq_gen.sh is a bash file that simulates DNA sequence 
+5- 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. 
 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 
-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\>
+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\>
 
 7- Run the following script to get the gene trees without the outgroup:
 Rscript get_inferred_gene_trees.R
@@ -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
 
-2. Root ASTRAL tree:
+2. Root the ASTRAL tree:
 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
 
-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
 
 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
 
 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`;
 do
   sh parse_network_subproblems.sh $path/$taxa/genetrees $i 
@@ -101,4 +98,4 @@ do
   Rscript select_network_Lscore_combine.R $path/$taxa/genetrees $numRep $i
 done
 
-9. Run merge.R to merge subproblems
+9. Run merge.R to merge subproblems into a phylogeny